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Zhu H, Zhu D, Wu K, He W, Li L, Li T, Liu L, Liu Z, Song X, Cheng W, Mo J, Yao Y, Li J. Establishment and evaluation of a qPCR method for the detection of pfmdr1 mutations in Plasmodium falciparum, the causal agent of fatal malaria. Diagn Microbiol Infect Dis 2024; 110:116400. [PMID: 38909426 DOI: 10.1016/j.diagmicrobio.2024.116400] [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: 04/02/2024] [Revised: 05/23/2024] [Accepted: 06/10/2024] [Indexed: 06/25/2024]
Abstract
Drug resistance surveillance is a major integral part of malaria control programs. Molecular methods play a pivotal role in drug resistance detection and related molecular research. This study aimed to develop a rapid and accurate detection method for drug resistance of Plasmodium falciparum (P. falciparum). A quantitative real-time PCR (qPCR) assay has been developed that identifies the mutation at locus A256T in the P.falciparum multi-drug resistance(pfmdr1) gene producing amino acid change at position 86. The results of 198 samples detected by qPCR were consistent with nested PCR and sequencing, giving an accuracy of 94.3%. The sensitivity, specificity, positive and negative predictive value of qPCR were 85.7%, 97.6%, 90.0% and 96.4%, respectively. The results of qPCR are basically consistent with the nested PCR, which is expected to replace the nested PCR as a new molecular biological method for drug resistance detection, providing reliable technical support for global malaria prevention and control.
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Affiliation(s)
- Huiyin Zhu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China; Department of Pediatrics, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, PR China
| | - Daiqian Zhu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Kai Wu
- Wuhan Centers for Disease Prevention and Control, Wuhan 430024, PR China
| | - Wei He
- Jiangnan University, Wuxi 442000, PR China
| | - Liugen Li
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Tongfei Li
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Long Liu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Zhixin Liu
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Xiaonan Song
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Weijia Cheng
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Jinyu Mo
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China
| | - Yi Yao
- Department of Pediatrics, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, PR China
| | - Jian Li
- Shiyan Key Laboratory of Virology, Hubei University of Medicine, Shiyan 442000, PR China.
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He W, Sendor R, Potlapalli VR, Kashamuka MM, Tshefu AK, Phanzu F, Kalonji A, Ngasala B, Thwai KL, Juliano JJ, Lin JT, Parr JB. Development of new real-time PCR assays for detection and species differentiation of Plasmodium ovale. PLoS Negl Trop Dis 2024; 18:e0011759. [PMID: 39255325 DOI: 10.1371/journal.pntd.0011759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 09/20/2024] [Accepted: 08/15/2024] [Indexed: 09/12/2024] Open
Abstract
BACKGROUND The parasite species Plasmodium ovalecurtisi (P. ovalecurtisi) and Plasmodium ovalewallikeri (P. ovalewallikeri), formerly known as Plasmodium ovale, are endemic across multiple African countries. These species are thought to differ in clinical symptomatology and latency, but only a small number of existing diagnostic assays can detect and distinguish them. In this study, we sought to develop new assays for the detection and differentiation of P. ovalecurtisi and P. ovalewallikeri by leveraging recently published whole-genome sequences for both species. METHODS Repetitive sequence motifs were identified in available P. ovalecurtisi and P. ovalewallikeri genomes and used for assay development and validation. We evaluated the analytical sensitivity of the best-performing singleplex and duplex assays using synthetic plasmids. We then evaluated the specificity of the duplex assay using a panel of samples from Tanzania and the Democratic Republic of the Congo (DRC), and validated its performance using 55 P. ovale samples and 40 non-ovale Plasmodium samples from the DRC. RESULTS The best-performing P. ovalecurtisi and P. ovalewallikeri targets had 9 and 8 copies within the reference genomes, respectively. The P. ovalecurtisi assay had high sensitivity with a 95% confidence lower limit of detection (LOD) of 3.6 parasite genome equivalents/μl, while the P. ovalewallikeri assay had a 95% confidence LOD of 25.9 parasite genome equivalents/μl. A duplex assay targeting both species had 100% specificity and 95% confidence LOD of 4.2 and 41.2 parasite genome equivalents/μl for P. ovalecurtisi and P. ovalewallikeri, respectively. CONCLUSIONS We identified promising multi-copy targets for molecular detection and differentiation of P. ovalecurtisi and P. ovalewallikeri and used them to develop real-time PCR assays. The best performing P. ovalecurtisi assay performed well in singleplex and duplex formats, while the P. ovalewallikeri assay did not reliably detect low-density infections in either format. These assays have potential use for high-throughput identification of P. ovalecurtisi, or for identification of higher density P. ovalecurtisi or P. ovalewallikeri infections that are amenable to downstream next-generation sequencing.
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Affiliation(s)
- Wenqiao He
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Rachel Sendor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Varun R Potlapalli
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Antoinette K Tshefu
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | | | | | - Billy Ngasala
- Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - Kyaw Lay Thwai
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jonathan J Juliano
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jessica T Lin
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jonathan B Parr
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Patel P, Mishra KK, Ghosh K. Confirmatory Assay for Laboratory Diagnosis of Malaria Using Molecular Approach. Acta Parasitol 2024; 69:1000-1004. [PMID: 38498250 DOI: 10.1007/s11686-024-00831-0] [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: 10/12/2022] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Prompt malarial treatment and surveillance is crucial for accurate diagnosis of Plasmodium Sp. Gold standard microscopic examination has been widely applied for diagnosis of malaria in most part of the endemic areas. But in case of submicroscopic and asymptomatic microscopic diagnosis is questioned. The study aims to develop a simple, cost effective & robust nucleic acid amplification technique for the detection of malaria parasite. METHODS Study population included 50 clinically diagnosed positive malaria patient samples from various pathological laboratories. Microscopy by preparing thick film was carried out of every sample for primary screening in the available facility of Surat Raktadan Kendra & Research Centre- Blood Bank. The conventional PCR (Polymerase Chain Reaction) was applied for genus-specific amplification targeting the 18 S rRNA gene of Plasmodium. Agarose gel electrophoresis was used to separate and analyze the amplified PCR product using 2% Agarose gel. RESULTS AND CONCLUSION The study shows that nested PCR not only detected all microscopic positive samples, but also detected submicroscopic infections that were missed or misread by microscopy. Hence, the sensitivity of molecular based detection technique is proved to be more compared to microscopic examination.
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Affiliation(s)
- Parizad Patel
- Surat Raktadan Kendra & Research Centre (Regional Blood Transfusion & Research Centre), Khatodara Health Centre, 1st Floor, Udhana Magdalla Road, Khatodara, Surat, Gujarat, 395002, India
| | - Kanchan Kumar Mishra
- Surat Raktadan Kendra & Research Centre (Regional Blood Transfusion & Research Centre), Khatodara Health Centre, 1st Floor, Udhana Magdalla Road, Khatodara, Surat, Gujarat, 395002, India
| | - Kanjaksha Ghosh
- Surat Raktadan Kendra & Research Centre (Regional Blood Transfusion & Research Centre), Khatodara Health Centre, 1st Floor, Udhana Magdalla Road, Khatodara, Surat, Gujarat, 395002, India
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Calderaro A, Piccolo G, Chezzi C. The Laboratory Diagnosis of Malaria: A Focus on the Diagnostic Assays in Non-Endemic Areas. Int J Mol Sci 2024; 25:695. [PMID: 38255768 PMCID: PMC10815132 DOI: 10.3390/ijms25020695] [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: 11/20/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Even if malaria is rare in Europe, it is a medical emergency and programs for its control should ensure both an early diagnosis and a prompt treatment within 24-48 h from the onset of the symptoms. The increasing number of imported malaria cases as well as the risk of the reintroduction of autochthonous cases encouraged laboratories in non-endemic countries to adopt diagnostic methods/algorithms. Microscopy remains the gold standard, but with limitations. Rapid diagnostic tests have greatly expanded the ability to diagnose malaria for rapid results due to simplicity and low cost, but they lack sensitivity and specificity. PCR-based assays provide more relevant information but need well-trained technicians. As reported in the World Health Organization Global Technical Strategy for Malaria 2016-2030, the development of point-of-care testing is important for the improvement of diagnosis with beneficial consequences for prompt/accurate treatment and for preventing the spread of the disease. Despite their limitations, diagnostic methods contribute to the decline of malaria mortality. Recently, evidence suggested that artificial intelligence could be utilized for assisting pathologists in malaria diagnosis.
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Affiliation(s)
- Adriana Calderaro
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (G.P.); (C.C.)
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LUUSE ARNOLDT, ALIDU HUSEINI, MAWULI1 MAWUSIADEPA, MUBARAK ABDULRAHMAN, GYAN BEN. Do Blood group and Sickle cell trait protect against placental malaria? J Public Health Afr 2023; 14:2817. [PMID: 38259428 PMCID: PMC10801398 DOI: 10.4081/jphia.2024.2817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Blood group O is reported to confer some degree of protection from severe malaria in endemic setting. This protection is believed to be due to reduced and smaller rosette formation in people of blood group O which can easily be cleared by the host immune system. Also, sickle cell trait (HbAS) is reported to disrupt the adhesion of infected erythrocytes to microvascular endothelial walls, which could protect pregnant women from placental malaria. We determined the association between HbAS and ABO blood group, and placental malaria amongst pregnant women of all parities. The study enrolled 221 pregnant women. Peripheral blood samples were taken for malaria smears, ABO blood grouping and haemoglobin (Hb) electrophoresis. A structured questionnaire was used to age, bed net usage, and the number of Sulphadoxine-pyrimethamine (SP) doses taken by a pregnant woman. Two hundred and twenty-one (221) pregnant women were enrolled and out of this number, 110 (49.8%) were primiparae and 111 (50.2%) multiparae, with a mean age of 23.7±5.2. Placental malaria (PM) prevalence by PCR detection was 19.4% (43/221). Of those who were malaria positive 58.1% (25/43) were primiparae. Primiparae who are of blood group O were more susceptible to PM [P=0.04, (OR); 2.85, 95% (Cl), 1.12-9.01]. But sickle cell trait did not reduce the prevalence of PM [P=0.84 (OR); 0.92, 95% (Cl), 0.43-1.99]. Non-blood group O primiparae women were protected against placental malaria. This could be why some primiparae women are protected from PM, just like multiparae women.
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Affiliation(s)
| | - HUSEINI ALIDU
- School of Allied Health Sciences, University of Health and Allied Sciences, Ho
| | - MAWUSI ADEPA MAWULI1
- Department of Biochemistry Cell and Molecular Biology, University of Ghana, Accra
- Department of Pathology, University of Ghana Medical School, College of Health Sciences, University of Ghana, Korle-Bu, Accra, Ghana
| | - ABDUL-RAHMAN MUBARAK
- West Africa Center for Cell Biology of Infectious Pathogens
- Department of Biochemistry Cell and Molecular Biology, University of Ghana, Accra
- Department of Pathology, University of Ghana Medical School, College of Health Sciences, University of Ghana, Korle-Bu, Accra, Ghana
| | - BEN GYAN
- Department of Biochemistry Cell and Molecular Biology, University of Ghana, Accra
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra
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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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Srisutham S, Rattanakoch P, Kijprasong K, Sugaram R, Kantaratanakul N, Srinulgray T, Dondorp AM, Imwong M. A novel sensitive hexaplex high-resolution melt assay for identification of five human Plasmodium species plus internal control. Acta Trop 2023; 248:107020. [PMID: 37739253 PMCID: PMC10641754 DOI: 10.1016/j.actatropica.2023.107020] [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: 06/28/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND The diagnosis of malaria infection in humans remains challenging, further complicated by mixed Plasmodium species infections, potentially altering disease severity and morbidity. To facilitate appropriate control measures and treatment, rapid, sensitive, and specific detection assays, including those for the second minor species, would be required. This study aimed to develop a multiplex high-resolution melting (hexaplex PCR-HRM) assay with seven distinct peaks corresponding to five Plasmodium species of the Plasmodium genus, and an internal control to limit false negatives providing quality assurance testing results. METHODS Five species-specific primers for human malaria species were designed targeting on the Plasmodium 18 small subunit ribosomal RNA (18S rRNA) and mitochondrial genes. The hexaplex PCR-HRM was developed for the simultaneous and rapid detection and differentiation of five human Plasmodium spp. The limit of detection (LoD), sensitivity, and specificity of the assay were evaluated. Artificial mixing was used to assess the ability to determine the second minor species. Furthermore, a hexaplex PCR-HRM assay was used to identify 120 Plasmodium-infected clinical isolates from Kanchanaburi, Western Thailand, where malaria is endemic. RESULTS The hexaplex PCR-HRM assay detected the targeted genome of five Plasmodium species at levels as low as 2.354-3.316 copies/uL with 91.76 % sensitivity and 98.04 % specificity. In artificial mixing, the assay could detect minority parasite species at 0.001 % of the predominant parasite population. Plasmodium vivax infections (99 %) accounted for the majority of malaria cases in Kanchanaburi, Thailand. CONCLUSIONS The developed hexaplex PCR-HRM assay we present in this study is a novel approach for multiplexing the Plasmodium genus and detecting five Plasmodium species with the advantage of detecting second minority parasite species. The developed one-step assay without any nesting protocols would reduce the risks of cross-contamination. Moreover, it also provides a simple, sensitive, specific, and low-cost approach for optional molecular detection of malaria.
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Affiliation(s)
- Suttipat Srisutham
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.
| | - Paweesuda Rattanakoch
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | | | - Rungniran Sugaram
- Division of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | | | | | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, Northern Ireland UK
| | - Mallika Imwong
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Pacheco Souza RS, Dos Reis MF, de Lima Ferreira LC, Morais MC, Lima AKS, Albuquerque Barbosa LR, de Melo GC, de Lacerda MVG. Standardization of DNA extraction from paraffinized spleen samples: molecular diagnosis of human malaria. Malar J 2023; 22:361. [PMID: 38012686 PMCID: PMC10683280 DOI: 10.1186/s12936-023-04764-3] [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: 07/26/2023] [Accepted: 10/22/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Plasmodium vivax is the main species responsible for human malaria in Brazil, and one of its manifestations is splenic malaria, though there are still challenges in its diagnosis. The present study aimed to standardize Plasmodium sp. DNA extraction from histological slices of spleen and diagnosis using real-time qPCR. METHODS This study performed a microtomy of a paraffin-embedded spleen as a positive control for P. vivax from a patient who had been previously diagnosed with the parasite. The sample was deparaffinized with xylol and ethanol, then DNA extraction was performed with two commercial kits. qPCR was carried out with the Taqman system for detection of Plasmodium sp. and was made species-specific using PvmtCOX1 gene. From 2015 to 2019, 200 spleen samples were obtained from trauma patients subjected to splenectomy in Manaus, Amazonas. All the samples were tested for cell-free human DNA (cfDNA). RESULTS The deparaffinization and the Plasmodium vivax DNA extraction method was successfully standardized, and the control sample was positive for P. vivax. Of the 200 samples, all qPCRs were negative, but they were positive for human PCR. CONCLUSION Paraffinization is practical and efficient for the preservation of samples, but the formation of bonds between proteins and DNA makes extraction difficult. Despite this, in this study, it was possible to standardize a method of DNA extraction for detecting P. vivax.
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Affiliation(s)
| | | | - Luiz Carlos de Lima Ferreira
- Amazonas State University (UEA), Manaus, Amazonas, 69040-000, Brazil
- Doctor Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Amazonas, 69040-000, Brazil
| | - Manuela C Morais
- Federal University of Amazonas, Manaus, Amazonas, 69080-900, Brazil
| | | | - Laila Rowena Albuquerque Barbosa
- Amazonas State University (UEA), Manaus, Amazonas, 69040-000, Brazil
- Doctor Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Amazonas, 69040-000, Brazil
| | - Gisely Cardoso de Melo
- Amazonas State University (UEA), Manaus, Amazonas, 69040-000, Brazil.
- Doctor Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Amazonas, 69040-000, Brazil.
| | - Marcus Vinicius Guimaraes de Lacerda
- Leonidas & Maria Deane Institute (ILMD), Fiocruz, Manaus, Amazonas, 69057-070, Brazil
- Doctor Heitor Vieira Dourado Tropical Medicine Foundation, Manaus, Amazonas, 69040-000, Brazil
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Mshani IH, Siria DJ, Mwanga EP, Sow BB, Sanou R, Opiyo M, Sikulu-Lord MT, Ferguson HM, Diabate A, Wynne K, González-Jiménez M, Baldini F, Babayan SA, Okumu F. Key considerations, target product profiles, and research gaps in the application of infrared spectroscopy and artificial intelligence for malaria surveillance and diagnosis. Malar J 2023; 22:346. [PMID: 37950315 PMCID: PMC10638832 DOI: 10.1186/s12936-023-04780-3] [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: 03/04/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Studies on the applications of infrared (IR) spectroscopy and machine learning (ML) in public health have increased greatly in recent years. These technologies show enormous potential for measuring key parameters of malaria, a disease that still causes about 250 million cases and 620,000 deaths, annually. Multiple studies have demonstrated that the combination of IR spectroscopy and machine learning (ML) can yield accurate predictions of epidemiologically relevant parameters of malaria in both laboratory and field surveys. Proven applications now include determining the age, species, and blood-feeding histories of mosquito vectors as well as detecting malaria parasite infections in both humans and mosquitoes. As the World Health Organization encourages malaria-endemic countries to improve their surveillance-response strategies, it is crucial to consider whether IR and ML techniques are likely to meet the relevant feasibility and cost-effectiveness requirements-and how best they can be deployed. This paper reviews current applications of IR spectroscopy and ML approaches for investigating malaria indicators in both field surveys and laboratory settings, and identifies key research gaps relevant to these applications. Additionally, the article suggests initial target product profiles (TPPs) that should be considered when developing or testing these technologies for use in low-income settings.
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Affiliation(s)
- Issa H Mshani
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - Doreen J Siria
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Emmanuel P Mwanga
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Bazoumana Bd Sow
- Department of Medical Biology and Public Health, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Roger Sanou
- Department of Medical Biology and Public Health, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Mercy Opiyo
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
- Malaria Elimination Initiative (MEI), Institute for Global Health Sciences, University of California, San Francisco, USA
| | - Maggy T Sikulu-Lord
- Faculty of Science, School of the Environment, The University of Queensland, Brisbane, QLD, Australia
| | - Heather M Ferguson
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Abdoulaye Diabate
- Department of Medical Biology and Public Health, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso, Burkina Faso
| | - Klaas Wynne
- School of Chemistry, The University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mario González-Jiménez
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
- School of Chemistry, The University of Glasgow, Glasgow, G12 8QQ, UK
| | - Francesco Baldini
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Simon A Babayan
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - Fredros Okumu
- Ifakara Health Institute, Environmental Health, and Ecological Sciences Department, Morogoro, United Republic of Tanzania.
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
- School of Life Sciences and Biotechnology, Nelson Mandela African Institution of Science and Technology, Arusha, United Republic of Tanzania.
- School of Public Health, The University of the Witwatersrand, Park Town, South Africa.
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10
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He W, Sendor R, Potlapalli VR, Kashamuka MM, Tshefu AK, Phanzu F, Kalonji A, Ngasala B, Thwai KL, Juliano JJ, Lin JT, Parr JB. A novel duplex qualitative real-time PCR assay for the detection and differentiation of Plasmodium ovale curtisi and Plasmodium ovale wallikeri malaria. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.31.23297819. [PMID: 37961397 PMCID: PMC10635243 DOI: 10.1101/2023.10.31.23297819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background P. ovale spp. infections are endemic across multiple African countries and are caused by two distinct non-recombining species, P. ovale curtisi (Poc) and P. ovale wallikeri (Pow). These species are thought to differ in clinical symptomatology and latency, but existing diagnostic assays have limited ability to detect and distinguish them. In this study, we developed a new duplex assay for the detection and differentiation of Poc and Pow that can be used to improve our understanding of these parasites. Methods Repetitive sequence motifs were identified in available Poc and Pow genomes and used for assay development and validation. We evaluated the analytical sensitivity and specificity of the best-performing assay using a panel of samples from Tanzania and the Democratic Republic of the Congo (DRC), then validated its performance using 55 P. ovale spp. samples and 40 non-ovale Plasmodium samples from the DRC. Poc and Pow prevalence among symptomatic individuals sampled across three provinces of the DRC were estimated. Results The best-performing Poc and Pow targets had 9 and 8 copies within the reference genomes, respectively. Our duplex assay had 100% specificity and 95% confidence lower limits of detection of 4.2 and 41.2 parasite genome equivalents/μl for Poc and Pow, respectively. Species was determined in 80% of all P. ovale spp.-positive field samples and 100% of those with >10 parasites/μl. Most P. ovale spp. field samples from the DRC were found to be Poc infections. Conclusions We identified promising multi-copy targets for molecular detection and differentiation of Poc and Pow and used them to develop a new duplex real-time PCR assay that performed well when applied to diverse field samples. Though low-density Pow infections are not reliably detected, the assay is highly specific and can be used for high-throughput studies of P. ovale spp. epidemiology among symptomatic cases in malaria-endemic countries like the DRC.
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Affiliation(s)
- Wenqiao He
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, China
| | - Rachel Sendor
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
| | - Varun R. Potlapalli
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | | | | | | | - Billy Ngasala
- Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - Kyaw Lay Thwai
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jonathan J. Juliano
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
| | - Jessica T. Lin
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jonathan B. Parr
- Division of Infectious Diseases and Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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11
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van Bergen KJM, Stuitje AR, Akkers RC, Vermeer HJ, Castel R, Mank TG. Performance of a novel melting curve-based qPCR assay for malaria parasites in routine clinical practice in non-endemic setting. Malar J 2023; 22:191. [PMID: 37349789 DOI: 10.1186/s12936-023-04617-z] [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: 03/05/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND High-quality malaria diagnosis is essential for effective treatment and clinical disease management. Microscopy and rapid diagnostic tests are the conventional methods performed as first-line malaria diagnostics in non-endemic countries. However, these methods lack the characteristic to detect very low parasitaemia, and accurate identification of the Plasmodium species can be difficult. This study evaluated the performance of the MC004 melting curve-based qPCR for the diagnosis of malaria in routine clinical practice in non-endemic setting. METHODS AND RESULTS Whole blood samples were collected from 304 patients with clinical suspicion of malaria and analysed by both the MC004 assay and conventional diagnostics. Two discrepancies were found between the MC004 assay and microscopy. Repeated microscopic analysis confirmed the qPCR results. Comparison of the parasitaemia of nineteen Plasmodium falciparum samples determined by both microscopy and qPCR showed the potential of the MC004 assay to estimate the parasite load of P. falciparum. Eight Plasmodium infected patients were followed after anti-malarial treatment by the MC004 assay and microscopy. The MC004 assay still detected Plasmodium DNA although no parasites were seen with microscopy in post-treatment samples. The rapid decline in Plasmodium DNA showed the potential for therapy-monitoring. CONCLUSION Implementation of the MC004 assay in non-endemic clinical setting improved the diagnosis of malaria. The MC004 assay demonstrated superior Plasmodium species identification, the ability to indicate the Plasmodium parasite load, and can potentially detect submicroscopic Plasmodium infections.
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Affiliation(s)
- Kim J M van Bergen
- Result Laboratorium, Albert Schweitzer Hospital, Albert Schweitzerplaats 25, 3300 AK, Dordrecht, The Netherlands.
| | - Antoine R Stuitje
- MRC Holland, Willem Schoutenstraat 1, 1057 DL, Amsterdam, The Netherlands
| | - Robert C Akkers
- Result Laboratorium, Albert Schweitzer Hospital, Albert Schweitzerplaats 25, 3300 AK, Dordrecht, The Netherlands
| | - Henricus J Vermeer
- Result Laboratorium, Albert Schweitzer Hospital, Albert Schweitzerplaats 25, 3300 AK, Dordrecht, The Netherlands
| | - Rob Castel
- Result Laboratorium, Albert Schweitzer Hospital, Albert Schweitzerplaats 25, 3300 AK, Dordrecht, The Netherlands
| | - Theo G Mank
- Regional Laboratory for Medical Microbiology and Public Health, Boerhaavelaan 26, 2035 RC, Haarlem, The Netherlands
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12
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Malpartida-Cardenas K, Moser N, Ansah F, Pennisi I, Ahu Prah D, Amoah LE, Awandare G, Hafalla JCR, Cunnington A, Baum J, Rodriguez-Manzano J, Georgiou P. Sensitive Detection of Asymptomatic and Symptomatic Malaria with Seven Novel Parasite-Specific LAMP Assays and Translation for Use at Point-of-Care. Microbiol Spectr 2023; 11:e0522222. [PMID: 37158750 PMCID: PMC10269850 DOI: 10.1128/spectrum.05222-22] [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: 12/20/2022] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
Human malaria is a life-threatening parasitic disease with high impact in the sub-Saharan Africa region, where 95% of global cases occurred in 2021. While most malaria diagnostic tools are focused on Plasmodium falciparum, there is a current lack of testing non-P. falciparum cases, which may be underreported and, if undiagnosed or untreated, may lead to severe consequences. In this work, seven species-specific loop-mediated isothermal amplification (LAMP) assays were designed and evaluated against TaqMan quantitative PCR (qPCR), microscopy, and enzyme-linked immunosorbent assays (ELISAs). Their clinical performance was assessed with a cohort of 164 samples of symptomatic and asymptomatic patients from Ghana. All asymptomatic samples with a parasite load above 80 genomic DNA (gDNA) copies per μL of extracted sample were detected with the Plasmodium falciparum LAMP assay, reporting 95.6% (95% confidence interval [95% CI] of 89.9 to 98.5) sensitivity and 100% (95% CI of 87.2 to 100) specificity. This assay showed higher sensitivity than microscopy and ELISA, which were 52.7% (95% CI of 39.7 to 67%) and 67.3% (95% CI of 53.3 to 79.3%), respectively. Nine samples were positive for P. malariae, indicating coinfections with P. falciparum, which represented 5.5% of the tested population. No samples were detected as positive for P. vivax, P. ovale, P. knowlesi, or P. cynomolgi by any method. Furthermore, translation to the point-of-care was demonstrated with a subcohort of 18 samples tested locally in Ghana using our handheld lab-on-chip platform, Lacewing, showing comparable results to a conventional fluorescence-based instrument. The developed molecular diagnostic test could detect asymptomatic malaria cases, including submicroscopic parasitemia, and it has the potential to be used for point-of-care applications. IMPORTANCE The spread of Plasmodium falciparum parasites with Pfhrp2/3 gene deletions presents a major threat to reliable point-of-care diagnosis with current rapid diagnostic tests (RDTs). Novel molecular diagnostics based on nucleic acid amplification are needed to address this liability. In this work, we overcome this challenge by developing sensitive tools for the detection of Plasmodium falciparum and non-P. falciparum species. Furthermore, we evaluate these tools with a cohort of symptomatic and asymptomatic malaria patients and test a subcohort locally in Ghana. The findings of this work could lead to the implementation of DNA-based diagnostics to fight against the spread of malaria and provide reliable, sensitive, and specific diagnostics at the point of care.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Nicolas Moser
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Ivana Pennisi
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Diana Ahu Prah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Linda Eva Amoah
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Gordon Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Julius Clemence R. Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Aubrey Cunnington
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jake Baum
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
- School of Biomedical Sciences, University of New South Wales Sydney, Sydney, Australia
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
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13
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Sendor R, Mitchell CL, Chacky F, Mohamed A, Mhamilawa LE, Molteni F, Nyinondi S, Kabula B, Mkali H, Reaves EJ, Serbantez N, Kitojo C, Makene T, Kyaw T, Muller M, Mwanza A, Eckert EL, Parr JB, Lin JT, Juliano JJ, Ngasala B. Similar Prevalence of Plasmodium falciparum and Non-P. falciparum Malaria Infections among Schoolchildren, Tanzania 1. Emerg Infect Dis 2023; 29:1143-1153. [PMID: 37209670 PMCID: PMC10202886 DOI: 10.3201/eid2906.221016] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
Achieving malaria elimination requires considering both Plasmodium falciparum and non-P. falciparum infections. We determined prevalence and geographic distribution of 4 Plasmodium spp. by performing PCR on dried blood spots collected within 8 regions of Tanzania during 2017. Among 3,456 schoolchildren, 22% had P. falciparum, 24% had P. ovale spp., 4% had P. malariae, and 0.3% had P. vivax infections. Most (91%) schoolchildren with P. ovale infections had low parasite densities; 64% of P. ovale infections were single-species infections, and 35% of those were detected in low malaria endemic regions. P. malariae infections were predominantly (73%) co-infections with P. falciparum. P. vivax was detected mostly in northern and eastern regions. Co-infections with >1 non-P. falciparum species occurred in 43% of P. falciparum infections. A high prevalence of P. ovale infections exists among schoolchildren in Tanzania, underscoring the need for detection and treatment strategies that target non-P. falciparum species.
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14
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Lin K, Wang S, Sui Y, Zhang T, Luo F, Shi F, Qian Y, Li J, Lu S, Cotter C, Wang D, Li S. Evaluation of an Innovative Point-of-Care Rapid Diagnostic Test for the Identification of Imported Malaria Parasites in China. Trop Med Infect Dis 2023; 8:296. [PMID: 37368714 DOI: 10.3390/tropicalmed8060296] [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: 02/19/2023] [Revised: 04/20/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND China was certified malaria-free by the World Health Organization on 30 June 2021. However, due to imported malaria, maintaining a malaria-free status in China is an ongoing challenge. There are critical gaps in the detection of imported malaria through the currently available tools, especially for non-falciparum malaria. In the study, a novel point-of-care Rapid Diagnostic Test designed for the detection of imported malaria infections was evaluated in the field. METHODS Suspected imported malaria cases reported from Guangxi and Anhui Provinces of China during 2018-2019 were enrolled to evaluate the novel RDTs. Diagnostic performance of the novel RDTs was evaluated based on its sensitivity, specificity, positive and negative predictive values, and Cohen's kappa coefficient, using polymerase chain reaction as the gold standard. The Additive and absolute Net Reclassification Index were calculated to compare the diagnostic performance between the novel RDTs and Wondfo RDTs (control group). RESULTS A total of 602 samples were tested using the novel RDTs. Compared to the results of PCR, the novel RDTs presented sensitivity, specificity, PPV, NPV, and diagnostic accuracy rates of 78.37%, 95.05%, 94.70%, 79.59%, and 86.21%, respectively. Among the positive samples, the novel RDTs found 87.01%, 71.31%, 81.82%, and 61.54% of P. falciparum, P. ovale, P. vivax, and P. malariae, respectively. The ability to detect non-falciparum malaria did not differ significantly between the novel and Wondfo RDTs (control group). However, Wondfo RDTs can detect more P. falciparum cases than the novel RDTs (96.10% vs. 87.01%, p < 0.001). After the introduction of the novel RDTs, the value of the additive and absolute Net Reclassification Index is 1.83% and 1.33%, respectively. CONCLUSIONS The novel RDTs demonstrated the ability to distinguish P. ovale and P. malariae from P. vivax which may help to improve the malaria post-elimination surveillance tools in China.
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Affiliation(s)
- Kangming Lin
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning 530028, China
| | - Shuqi Wang
- Anhui Provincial Center for Disease Control and Prevention, Hefei 230601, China
| | - Yuan Sui
- Brown School, Washington University, St. Louis, MO 63130, USA
| | - Tao Zhang
- Anhui Provincial Center for Disease Control and Prevention, Hefei 230601, China
| | - Fei Luo
- Chongqing Center for Disease Control and Prevention, Chongqing 400042, China
| | - Feng Shi
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Yingjun Qian
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Jun Li
- Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning 530028, China
| | - Shenning Lu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Chris Cotter
- Malaria Elimination Initiative, Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA 94109, USA
- Department of Women's and Children's Health, Uppsala University, 75309 Uppsala, Sweden
| | - Duoquan Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 201100, China
| | - Shizhu Li
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 201100, China
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15
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Tripathi H, Bhalerao P, Singh S, Arya H, Alotaibi BS, Rashid S, Hasan MR, Bhatt TK. Malaria therapeutics: are we close enough? Parasit Vectors 2023; 16:130. [PMID: 37060004 PMCID: PMC10103679 DOI: 10.1186/s13071-023-05755-8] [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: 01/06/2023] [Accepted: 03/22/2023] [Indexed: 04/16/2023] Open
Abstract
Malaria is a vector-borne parasitic disease caused by the apicomplexan protozoan parasite Plasmodium. Malaria is a significant health problem and the leading cause of socioeconomic losses in developing countries. WHO approved several antimalarials in the last 2 decades, but the growing resistance against the available drugs has worsened the scenario. Drug resistance and diversity among Plasmodium strains hinder the path of eradicating malaria leading to the use of new technologies and strategies to develop effective vaccines and drugs. A timely and accurate diagnosis is crucial for any disease, including malaria. The available diagnostic methods for malaria include microscopy, RDT, PCR, and non-invasive diagnosis. Recently, there have been several developments in detecting malaria, with improvements leading to achieving an accurate, quick, cost-effective, and non-invasive diagnostic tool for malaria. Several vaccine candidates with new methods and antigens are under investigation and moving forward to be considered for clinical trials. This article concisely reviews basic malaria biology, the parasite's life cycle, approved drugs, vaccine candidates, and available diagnostic approaches. It emphasizes new avenues of therapeutics for malaria.
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Affiliation(s)
- Himani Tripathi
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, 305817, Rajasthan, India
| | - Preshita Bhalerao
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, 305817, Rajasthan, India
| | - Sujeet Singh
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, 305817, Rajasthan, India
| | - Hemant Arya
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, 305817, Rajasthan, India.
| | - Bader Saud Alotaibi
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Alquwayiyah, Shaqra University, Riyadh, 11971, Saudi Arabia
| | - Summya Rashid
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj, 11942, Saudi Arabia
| | - Mohammad Raghibul Hasan
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, Alquwayiyah, Shaqra University, Riyadh, 11971, Saudi Arabia.
| | - Tarun Kumar Bhatt
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, 305817, Rajasthan, India.
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16
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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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Kshirsagar A, Choi G, Santosh V, Harvey T, Bernhards RC, Guan W. Handheld Purification-Free Nucleic Acid Testing Device for Point-of-Need Detection of Malaria from Whole Blood. ACS Sens 2023; 8:673-683. [PMID: 36696460 PMCID: PMC11214673 DOI: 10.1021/acssensors.2c02169] [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] [Indexed: 01/26/2023]
Abstract
World Health Organization's aim to eliminate malaria from developing/resource-limited economies requires easy access to low-cost, highly sensitive, and specific screening. We present a handheld nucleic acid testing device with on-chip automated sample preparation to detect malaria (Plasmodium falciparum) infection from a whole blood sample as a feasibility study. We used a simple two-reagent-based purification-free protocol to prepare the whole blood sample on a piezo pump pressure-driven microfluidic cartridge. The cartridge includes a unique mixing chamber for sample preparation and metering structures to dispense a predetermined volume of the sample lysate mixture into four chambers containing a reaction mix. The parasite genomic DNA concentration can be estimated by monitoring the fluorescence generated from the loop-mediated isothermal amplification reaction in real time. We achieved a sensitivity of ∼0.42 parasite/μL of whole blood, sufficient for detecting asymptomatic malaria parasite carriers.
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Affiliation(s)
- Aneesh Kshirsagar
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
| | - Gihoon Choi
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
| | - Vishaka Santosh
- U.S. Army, DEVCOM Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA
| | - Tara Harvey
- U.S. Army, DEVCOM Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA
| | - Robert Cory Bernhards
- U.S. Army, DEVCOM Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA
| | - Weihua Guan
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
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18
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Xiang Z, Li D, Wang S, Shen T, He W, Li M, Zeng W, Chen X, Wu Y, Cui L, Yang Z. A simple alkali lysis method for Plasmodium falciparum DNA extraction from filter paper blood samples. Mol Biochem Parasitol 2023; 254:111557. [PMID: 36822514 DOI: 10.1016/j.molbiopara.2023.111557] [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: 09/04/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023]
Abstract
A fast, simple, easy, efficient, and inexpensive method for DNA extraction from malaria parasites collected on filter paper would be very useful for molecular surveillance. The quality and quantity of DNA are critical to molecular diagnosis and analysis. Here, we developed a simple alkali lysis method for DNA extraction from blood samples on filter paper. The results showed that 10-50 mM NaOH and deionized water all effectively isolated parasite DNA at higher parasitemia, as witnessed by successful PCR amplification, while at a parasitemia of 0.01%, the 10 mM NaOH lysis condition generated the best results. Furthermore, DNA extracted by this method was successfully used to amplify a fragment of > 2000 bp. This method successfully extracted DNA from 1 µl of blood at a parasitemia as low as 0.0001% (equivalent to 5 parasites /µl). The DNA isolated by the 10 mM NaOH lysis method was stable to yield PCR products after storage at 4 °C or - 20 °C for 12 months. These results indicate that this alkali lysis method is simple, effective, sensitive, and inexpensive for isolating stable Plasmodium DNA from dried blood spots on filter paper.
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Affiliation(s)
- Zheng Xiang
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming 650500, Yunnan, China.
| | - Danlin Li
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Siqi Wang
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Ting Shen
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Wen He
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Mier Li
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Xi Chen
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Yanrui Wu
- Department of Cell Biology & Genetics, Kunming Medical University, Kunming 650500, Yunnan, China
| | - Liwang Cui
- Department of Internal Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Faculty of Basic Medical Science, Kunming Medical University, Kunming 650500, Yunnan, China.
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Survey of malaria vectors on the Cambodia, Thailand and China-Laos Borders. Malar J 2022; 21:399. [PMID: 36585690 PMCID: PMC9801360 DOI: 10.1186/s12936-022-04418-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 12/15/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Anopheles maculatus, Anopheles minimus and Anopheles dirus are the major vectors of malaria transmission in the Greater Mekong Subregion (GMS). The malaria burden in this region has decreased significantly in recent years as all GMS countries progress towards malaria elimination. It is necessary to investigate the Anopheles diversity and abundance status and assess the Plasmodium infection rates to understand the malaria transmission potential of these vector species in GMS countries to guide the development of up-to-date vector control strategies and interventions. METHODS A survey of mosquitoes was conducted in Stung Treng, Sainyabuli and Phongsaly Provinces on the Cambodia-Laos, Thailand-Laos and China-Laos borders, respectively. Mosquito collection was done by overnight trapping at sentinel sites in each province. After morphological identification, the 18S rRNA-based nested-PCR was performed to detect malaria parasites in the captured Anopheles mosquitoes. RESULTS A total of 18 965 mosquitoes comprising of 35 species of 2 subgenera (Subgenus Anopheles and Subgenus Cellia) and 4 tribes (Tribes Culicini, Aedini, Armigerini and Mansoniini) were captured. Tribe Culicini accounted for 85.66% of captures, followed by Subgenus Anopheles (8.15%). Anopheles sinensis dominated the Subgenus Anopheles by 99.81%. Plasmodium-infection was found in 25 out of the 1 683 individual or pooled samples of Anopheles. Among the 25 positive samples, 19, 5 and 1 were collected from Loum, Pangkhom and Siem Pang village, respectively. Eight Anopheles species were found infected with Plasmodium, i.e., An. sinensis, Anopheles kochi, Anopheles vagus, An. minimus, Anopheles annularis, Anopheles philippinensis, Anopheles tessellatus and An. dirus. The infection rates of Plasmodium falciparum, Plasmodium vivax and mixture of Plasmodium parasite species were 0.12% (2/1 683), 1.31% (22/1 683) and 0.06% (1/1 683), respectively. CONCLUSIONS Overall, this survey re-confirmed that multiple Anopheles species carry malaria parasites in the international border areas of the GMS countries. Anopheles sinensis dominated the Anopheles collections and as carriers of malaria parasites, therefore may play a significant role in malaria transmission. More extensive investigations of malaria vectors are required to reveal the detailed vector biology, ecology, behaviour, and genetics in GMS regions in order to assist with the planning and implementation of improved malaria control strategies.
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Ashraf S, Khalid A, de Vos AL, Feng Y, Rohrbach P, Hasan T. Malaria Detection Accelerated: Combing a High-Throughput NanoZoomer Platform with a ParasiteMacro Algorithm. Pathogens 2022; 11:pathogens11101182. [PMID: 36297240 PMCID: PMC9606851 DOI: 10.3390/pathogens11101182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/05/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Eradication of malaria, a mosquito-borne parasitic disease that hijacks human red blood cells, is a global priority. Microscopy remains the gold standard hallmark for diagnosis and estimation of parasitemia for malaria, to date. However, this approach is time-consuming and requires much expertise especially in malaria-endemic countries or in areas with low-density malaria infection. Thus, there is a need for accurate malaria diagnosis/parasitemia estimation with standardized, fast, and more reliable methods. To this end, we performed a proof-of-concept study using the automated imaging (NanoZoomer) platform to detect the malarial parasite in infected blood. The approach can be used as a steppingstone for malaria diagnosis and parasitemia estimation. Additionally, we created an algorithm (ParasiteMacro) compatible with free online imaging software (ImageJ) that can be used with low magnification objectives (e.g., 5×, 10×, and 20×) both in the NanoZoomer and routine microscope. The novel approach to estimate malarial parasitemia based on modern technologies compared to manual light microscopy demonstrated 100% sensitivity, 87% specificity, a 100% negative predictive value (NPV) and a 93% positive predictive value (PPV). The manual and automated malaria counts showed a good Pearson correlation for low- (R2 = 0.9377, r = 0.9683 and p < 0.0001) as well as high- parasitemia (R2 = 0.8170, r = 0.9044 and p < 0.0001) with low estimation errors. Our robust strategy that identifies and quantifies malaria can play a pivotal role in disease control strategies.
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Affiliation(s)
- Shoaib Ashraf
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 40 Blossom Street, Boston, MA 02114, USA
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X3V9, Canada
| | - Areeba Khalid
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 40 Blossom Street, Boston, MA 02114, USA
- Department of Computer Science, Mathematics Adelphi University, Garden City, NY 11530, USA
- Department of Biomedical Engineering, Tufts University, Medford, OR 02155, USA
| | - Arend L. de Vos
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 40 Blossom Street, Boston, MA 02114, USA
- Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Yanfang Feng
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 40 Blossom Street, Boston, MA 02114, USA
| | - Petra Rohrbach
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC H9X3V9, Canada
| | - Tayyaba Hasan
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 40 Blossom Street, Boston, MA 02114, USA
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Correspondence:
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Sivaradjy M, Hamide A, Krishnamoorthy S, Rajkumari N, Mohan V, Sharmila FM. Assessment of Plasmodium falciparum histidine rich protein 2 and /3 ( pfhrp 2&/ pfhrp 3) gene deletion or mutation in Plasmodium falciparum positive blood samples in a tertiary care centre in South India. J Parasit Dis 2022; 46:729-743. [PMID: 36091262 PMCID: PMC9458806 DOI: 10.1007/s12639-022-01492-4] [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: 12/29/2021] [Accepted: 04/18/2022] [Indexed: 10/18/2022] Open
Abstract
Rapid diagnostic card tests (RDTs) enable timely and appropriate diagnosis of malaria especially in remote areas. Plasmodium falciparum histidine rich protein 2 (PFHRP2) is the most targeted antigen for the detection of Plasmodium falciparum infections by rapid diagnostic card test. Genetic mutations and gene deletions are important emerging factors for false-negative RDTs, which may delay the provision of life-saving treatment for the patients. Hence, we would like to evaluate for the existence of pfhrp2/3 gene deleted P. falciparum parasites in our health care setting. This study was conducted for a period of 2 years in a tertiary care centre in South India. Blood samples that are microscopically confirmed as P. falciparum but negative by RDT were assessed for the presence of pfhrp2, pfhrp3, and their flanking genes using conventional PCR. Follow up of the clinical outcomes were also done for these patients. Of the 63 positive samples collected (50 /63) 79.4% were P.vivax and (13/63) 20.6% were P.falciparum by PCR. Among the 13 P. falciparum positive samples, 4 samples (4/13), (95% CI -10.36% to 61.11%) were found to be RDT negative but microscopically positive.Pfhrp2,pfhrp3 and their flanking genes were amplified for these 4 samples. All 4 samples were found to be negative for both pfhrp2-2 & pfhrp2-3 exon regions and also varying patterns of flanking gene deletions were also noted.This study provides molecular evidence for the existence of pfhrp2 & pfhrp3 deleted P. falciparum parasites in a tertiary care centre in South India warranting periodic evaluation of pfhrp2 based RDT use. Only pfhrp2/3 RDT based decision on diagnosis of P.falciparum malaria should always be reconsidered especially in remote areas.
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Affiliation(s)
- Monika Sivaradjy
- Department of Microbiology, JIPMER, Dhanvantri nagar, Puducherry, India
| | - Abdoul Hamide
- Department of Medicine, JIPMER, Dhanvantri nagar, Puducherry, India
| | | | - Nonika Rajkumari
- Department of Microbiology, JIPMER, Dhanvantri nagar, Puducherry, India
| | - Vamsi Mohan
- Department of Microbiology, JIPMER, Dhanvantri nagar, Puducherry, India
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Monteiro W, Karl S, Kuehn A, Almeida A, White M, Vitor-Silva S, Melo G, Brito-Sousa JD, Baia-da-Silva DC, Silva-Neto AV, Sampaio V, Bassat Q, Felger I, Mueller I, Lacerda M. Prevalence and force of Plasmodium vivax blood-stage infection and associated clinical malaria burden in the Brazilian Amazon. Mem Inst Oswaldo Cruz 2022; 117:e210330. [PMID: 35766676 PMCID: PMC9239689 DOI: 10.1590/0074-02760210330] [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: 10/11/2021] [Accepted: 05/16/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Understanding the epidemiology of malaria through the molecular force of the blood-stage infection of Plasmodium vivax (molFOB) may provide a detailed assessment of malaria transmission. OBJECTIVES In this study, we investigated risk factors and spatial-temporal patterns of incidence of Plasmodium infection and clinical malaria episodes in three peri-urban communities of Manaus, Western Brazilian Amazon. METHODS Monthly samples were collected in a cohort of 1,274 individuals between April 2013 and March 2014. DNA samples were subject to Plasmodium species. molFOB was calculated by counting the number of genotypes observed on each visit, which had not been present in the preceding two visits and adjusting these counts by the respective times-at-risk. FINDINGS Respectively, 77.8% and 97.2% of the population remained free of P. vivax and P. falciparum infection. Expected heterozygosity for P. vivax was 0.69 for MSP1_F3 and 0.86 for MS2. Multiplicity of infection in P. vivax was close to the value of 1. The season was associated with P. vivax positivity [adjusted hazard ratio (aHR) 2.6 (1.9-5.7)] and clinical disease [aHR 10.6 (2.4-47.2)]. P. falciparum infection was associated with previous malarial episodes [HR 9.7 (4.5-20.9)]. Subjects who reported possession of a bed net [incidence rate ratio (IRR) 1.6 (1.2-2.2)] or previous malaria episodes [IRR 3.0 (2.0-4.5)] were found to have significantly higher P. vivax molFOB. MAIN CONCLUSIONS Overall, P. vivax infection prevailed in the area and infections were mostly observed as monoclonal. Previous malaria episodes were associated with significantly higher P. vivax molFOB.
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Sedda L, McCann RS, Kabaghe AN, Gowelo S, Mburu MM, Tizifa TA, Chipeta MG, van den Berg H, Takken W, van Vugt M, Phiri KS, Cain R, Tangena JAA, Jones CM. Hotspots and super-spreaders: Modelling fine-scale malaria parasite transmission using mosquito flight behaviour. PLoS Pathog 2022; 18:e1010622. [PMID: 35793345 PMCID: PMC9292116 DOI: 10.1371/journal.ppat.1010622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 07/18/2022] [Accepted: 05/27/2022] [Indexed: 11/19/2022] Open
Abstract
Malaria hotspots have been the focus of public health managers for several years due to the potential elimination gains that can be obtained from targeting them. The identification of hotspots must be accompanied by the description of the overall network of stable and unstable hotspots of malaria, especially in medium and low transmission settings where malaria elimination is targeted. Targeting hotspots with malaria control interventions has, so far, not produced expected benefits. In this work we have employed a mechanistic-stochastic algorithm to identify clusters of super-spreader houses and their related stable hotspots by accounting for mosquito flight capabilities and the spatial configuration of malaria infections at the house level. Our results show that the number of super-spreading houses and hotspots is dependent on the spatial configuration of the villages. In addition, super-spreaders are also associated to house characteristics such as livestock and family composition. We found that most of the transmission is associated with winds between 6pm and 10pm although later hours are also important. Mixed mosquito flight (downwind and upwind both with random components) were the most likely movements causing the spread of malaria in two out of the three study areas. Finally, our algorithm (named MALSWOTS) provided an estimate of the speed of malaria infection progression from house to house which was around 200-400 meters per day, a figure coherent with mark-release-recapture studies of Anopheles dispersion. Cross validation using an out-of-sample procedure showed accurate identification of hotspots. Our findings provide a significant contribution towards the identification and development of optimal tools for efficient and effective spatio-temporal targeted malaria interventions over potential hotspot areas.
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Affiliation(s)
- Luigi Sedda
- Lancaster Ecology and Epidemiology Group, Lancaster Medical School, Lancaster University, United Kingdom
| | - Robert S. McCann
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
- School of Global and Public Health, Kamuzu University of Health Sciences, Blantyre, Malawi
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Alinune N. Kabaghe
- School of Global and Public Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Steven Gowelo
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
- School of Global and Public Health, Kamuzu University of Health Sciences, Blantyre, Malawi
- MAC Communicable Diseases Action Centre, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Monicah M. Mburu
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
- School of Global and Public Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Tinashe A. Tizifa
- School of Global and Public Health, Kamuzu University of Health Sciences, Blantyre, Malawi
- Center for Tropical Medicine and Travel Medicine, University of Amsterdam, The Netherlands
| | - Michael G. Chipeta
- School of Global and Public Health, Kamuzu University of Health Sciences, Blantyre, Malawi
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Henk van den Berg
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Willem Takken
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Michèle van Vugt
- Center for Tropical Medicine and Travel Medicine, University of Amsterdam, The Netherlands
| | - Kamija S. Phiri
- School of Global and Public Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Russell Cain
- Lancaster Ecology and Epidemiology Group, Lancaster Medical School, Lancaster University, United Kingdom
| | - Julie-Anne A. Tangena
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Christopher M. Jones
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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Costa GL, Alvarenga DAM, Aguiar ACC, Louzada J, Pereira DB, de Oliveira TF, Fonseca Júnior AA, Carvalho LH, Ferreira Alves de Brito C, Nóbrega de Sousa T. Improving the Molecular Diagnosis of Malaria: Droplet Digital PCR-Based Method Using Saliva as a DNA Source. Front Microbiol 2022; 13:882530. [PMID: 35633683 PMCID: PMC9136408 DOI: 10.3389/fmicb.2022.882530] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/20/2022] [Indexed: 12/20/2022] Open
Abstract
Malaria is an acute febrile disease caused by a protozoan of the genus Plasmodium. Light microscopy (LM) is the gold standard for the diagnosis of malaria. Despite this method being rapid and inexpensive, it has a low limit of detection, which hampers the identification of low parasitemia infections. By using multicopy targets and highly sensitive molecular techniques, it is possible to change this scenario. In this study, we evaluated the performance of droplet digital PCR (ddPCR) to detect Plasmodium DNA obtained from saliva samples (whole saliva and buccal swab) of 157 individuals exposed to malaria transmission from the Brazilian Amazon region. We used the highly sensitive ddPCR method with non-ribosomal multicopy targets for Plasmodium vivax (Pvr47) and Plasmodium falciparum (Pfr364). There was good concordance between the quantitative real-time PCR (qPCR) results from the saliva and blood, except for mixed-species infections. The sensitivity of qPCR was 93% for blood, 77% for saliva, and 47% for swabs. Parasite DNA was not detected in saliva samples in low-density infections compared with the detection in blood samples. ddPCR showed increased sensitivity for detecting Plasmodium in the blood and swabs (99% in blood, 73% in saliva, and 59% in swabs). Notably, ddPCR detected more mixed infections in the blood (15%), saliva (9%), and swabs (18%) than qPCR. Our data showed that the differences between ddPCR and qPCR were the result of a higher number of P. falciparum infections detected by ddPCR. Overall, there was a moderate correlation between parasite densities estimated by the different methods in the blood. Our findings highlight the possibility of using non-invasive sample collection methods for malaria diagnosis by targeting multicopy sequences combined with highly sensitive molecular methods.
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Affiliation(s)
- Gabriel Luíz Costa
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Denise Anete Madureira Alvarenga
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | | | - Jaime Louzada
- Health Sciences Center, Federal University of Roraima, Boa Vista, Brazil
| | | | | | | | - Luzia Helena Carvalho
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Cristiana Ferreira Alves de Brito
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Taís Nóbrega de Sousa
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
- *Correspondence: Taís Nóbrega de Sousa
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25
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Schneider R, Lamien-Meda A, Auer H, Wiedermann-Schmidt U, Chiodini PL, Walochnik J. A Rapid FRET Real-Time PCR Protocol for Simultaneous Quantitative Detection and Discrimination of Human Plasmodium Parasites. Bio Protoc 2022; 12:e4381. [PMID: 35530518 PMCID: PMC9018429 DOI: 10.21769/bioprotoc.4381] [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: 03/02/2022] [Revised: 12/23/2021] [Accepted: 03/07/2022] [Indexed: 12/29/2022] Open
Abstract
Malaria is the most important parasitic disease worldwide, and accurate diagnosis and treatment without delay are essential for reducing morbidity and mortality, especially in P. falciparum malaria. Real-time PCR is highly sensitive and highly specific, therefore an excellent diagnostic tool for laboratory detection and species-specific diagnosis of malaria, especially in non-endemic regions where experience in microscopic malaria diagnostics is limited. In contrast to many other real-time PCR protocols, our new fluorescence resonance energy transfer-based real-time PCR (FRET-qPCR) allows the quantitative and species-specific detection of all human Plasmodium spp. in one run. Species identification is based on single nucleotide polymorphisms (SNPs) within the MalFL probe, detectable by melting curve analysis. A significant advantage of our FRET-qPCR is the short turn-around time of less than two hours, including DNA extraction, which qualifies it for routine diagnostics. Rapid and reliable species-specific malaria diagnosis is important, because treatment is species-dependent. Apart from first-line diagnosis, the quantitative results of our new FRET-qPCR can be helpful in therapy control, to detect early treatment failure. Graphic abstract.
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Affiliation(s)
- Renate Schneider
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria
| | - Aline Lamien-Meda
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria
| | - Herbert Auer
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria
| | - Ursula Wiedermann-Schmidt
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria
| | | | - Julia Walochnik
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria
,
*For correspondence:
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Christensen P, Bozdech Z, Watthanaworawit W, Imwong M, Rénia L, Malleret B, Ling C, Nosten F. Reverse transcription PCR to detect low density malaria infections. Wellcome Open Res 2022; 6:39. [PMID: 35592834 PMCID: PMC9086519 DOI: 10.12688/wellcomeopenres.16564.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Targeted malaria elimination strategies require highly sensitive tests to detect low density malaria infections (LDMI). Commonly used methods for malaria diagnosis such as light microscopy and antigen-based rapid diagnostic tests (RDTs) are not sensitive enough for reliable identification of infections with parasitaemia below 200 parasites per milliliter of blood. While targeted malaria elimination efforts on the Thailand-Myanmar border have successfully used high sample volume ultrasensitive quantitative PCR (uPCR) to determine malaria prevalence, the necessity for venous collection and processing of large quantities of patient blood limits the widespread tractability of this method. Methods: Here we evaluated a real-time reverse transcription PCR (RT-qPCR) method that reduces the required sample volume compared to uPCR. To do this, 304 samples collected from an active case detection program in Kayin state, Myanmar were compared using uPCR and RT-qPCR. Results: Plasmodium spp. RT-qPCR confirmed 18 of 21 uPCR Plasmodium falciparum positives, while P. falciparum specific RT-qPCR confirmed 17 of the 21 uPCR P. falciparum positives. Combining both RT-qPCR results increased the sensitivity to 100% and specificity was 95.1%. Conclusion: Malaria detection in areas of low transmission and LDMI can benefit from the increased sensitivity of ribosomal RNA detection by RT-PCR, especially where sample volume is limited. Isolation of high quality RNA also allows for downstream analysis of malaria transcripts.
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Affiliation(s)
- Peter Christensen
- Shoklo Malaria Research Unit, Mahidol University, Maesot, Tak, 63110, Thailand
- Microbiology and Immunology, University of Otago, Dunedin, Otago, 9016, New Zealand
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Laurent Rénia
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
- A*STAR ID Labs, A*STAR, Singapore, 138648, Singapore
| | - Benoît Malleret
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
- Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Clare Ling
- Shoklo Malaria Research Unit, Mahidol University, Maesot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol University, Maesot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Zhang C, Luo C, Yang R, Yang Y, Guo X, Deng Y, Zhou H, Zhang Y. Morphological and molecular identification reveals a high diversity of Anopheles species in the forest region of the Cambodia-Laos border. Parasit Vectors 2022; 15:94. [PMID: 35303948 PMCID: PMC8933986 DOI: 10.1186/s13071-022-05167-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/17/2022] [Indexed: 11/25/2022] Open
Abstract
Background To develop an effective malaria vector intervention method in forested international border regions within the Greater Mekong Subregion (GMS), more in-depth studies should be conducted on local Anopheles species composition and bionomic features. There is a paucity of comprehensive surveys of biodiversity integrating morphological and molecular species identification conducted within the border of Laos and Cambodia. Methods A total of 2394 adult mosquitoes were trapped in the Cambodia–Laos border region. We first performed morphological identification of Anopheles mosquitoes and subsequently performed molecular identification using 412 recombinant DNA–internal transcribed spacer 2 (rDNA-ITS2) and 391 mitochondrial DNA–cytochrome c oxidase subunit 2 (mtDNA-COII) sequences. The molecular and morphological identification results were compared, and phylogenetic analysis of rDNA-ITS2 and mtDNA-COII was conducted for the sequence divergence among species. Results Thirteen distinct species of Anopheles were molecularly identified in a 26,415 km2 border region in Siem Pang (Cambodia) and Pathoomphone (Laos). According to the comparisons of morphological and molecular identity, the interpretation of local species composition for dominant species in the Cambodia–Laos border (An. dirus, An. maculatus, An. philippinensis, An. kochi and An. sinensis) achieved the highest accuracy of morphological identification, from 98.37 to 100%. In contrast, the other species which were molecularly identified were less frequently identified correctly (0–58.3%) by morphological methods. The average rDNA-ITS2 and mtDNA-COII interspecific divergence was respectively 318 times and 15 times higher than their average intraspecific divergence. The barcoding gap ranged from 0.042 to 0.193 for rDNA-ITS2, and from 0.033 to 0.047 for mtDNA-COII. Conclusions The Cambodia–Laos border hosts a high diversity of Anopheles species. The morphological identification of Anopheles species provides higher accuracy for dominant species than for other species. Molecular methods combined with morphological analysis to determine species composition, population dynamics and bionomic characteristics can facilitate a better understanding of the factors driving malaria transmission and the effects of interventions, and can aid in achieving the goal of eliminating malaria. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05167-0.
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Affiliation(s)
- Canglin Zhang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Chunhai Luo
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Rui Yang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Yaming Yang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Xiaofang Guo
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Yan Deng
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China
| | - Hongning Zhou
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu'er, 665099, People's Republic of China.
| | - Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China.
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Zhang Y, Zhang C, Yang R, Luo C, Deng Y, Liu Y, Zhang Y, Zhou H, Zhang D. Molecular phylogeny of Anopheles nivipes based on mtDNA-COII and mosquito diversity in Cambodia-Laos border. Malar J 2022; 21:91. [PMID: 35300704 PMCID: PMC8932176 DOI: 10.1186/s12936-022-04121-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 03/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Few studies have been conducted to investigate the distribution of mosquito vectors and the population structure of secondary vectors in the border region of Cambodia-Laos. The aim of this work was to study the mosquito diversity and molecular phylogeny of secondary vectors, i.e., Anopheles nivipes in this area. METHODS 1440 adult mosquitoes were trapped in the Cambodia-Laos border. mtDNA-COII were amplified and sequenced from 53 An. nivipes DNA samples. Together with COII sequences deposited in GenBank, a total of 86 COII sequences were used for examining population variations, genetic differentiation, spatial population structure, population expansion, and gene flow patterns. RESULTS The adult mosquitoes were classified into 5 genera and 27 species in this border region. The predominant genera were Culex (60.07%, 865/1440) and Anopheles (31.25%, 450/1440), and the major Anopheles species were An. nivipes (73.56%, 331/450) and Anopheles maculatus (14.22%, 64/450). Based on sequences analysis of COII, a high level of genetic differentiation was reported in two Northwest India (Cheema and Bathinda, Punjab) and Cambodia-Laos (Siem Pang, Stung treng) populations (FST = 0.97824, 0.97343, P < 0.05), as well as lower gene flow (Nm = 0.01112, 0.01365) in the An. nivipes populations. Phylogenetic analysis and SAMOVA revealed a gene barrier restricting gene flow among three An. nivipes populations. Mantel test suggested a significant correlation between geography and gene distance in all An. nivipes populations (Z = 44,983.1865, r = 0.5575, P = 0.0070). Neutrality test and Mismatch distribution revealed a recent population expansion of An. nivipes in the Cambodia-Laos population. CONCLUSIONS Anopheles nivipes was one of the major Anopheles species in the Cambodia-Laos border. Based on sequences analysis of COII, a genetic barrier between Cambodia-Laos and two Indian populations was found, and a recent population expanding or selecting of An. nivipes occurred in the Cambodia-Laos population, suggesting that COII might be an effective marker for describing the molecular phylogeny of An. nivipes. Further investigation and continuous surveillance of An. nivipes are warranted in this region.
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Affiliation(s)
- Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China
| | - Canglin Zhang
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Rui Yang
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Chunhai Luo
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Yan Deng
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Yan Liu
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China
| | - Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China.
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Center of Malaria Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Pu'er, 665099, China.
| | - Dongmei Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China.
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Zhao Y, Zhao Y, Sun Y, Fan L, Wang D, Wang H, Sun X, Zheng Z. A direct, sensitive and high-throughput genus and species-specific molecular assay for large-scale malaria screening. Infect Dis Poverty 2022; 11:25. [PMID: 35255983 PMCID: PMC8900325 DOI: 10.1186/s40249-022-00948-2] [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: 10/14/2021] [Accepted: 02/17/2022] [Indexed: 12/26/2022] Open
Abstract
Background Infectious disease diagnostics often requires sensitive molecular assays that identify at both genus and species levels. For large scale screening, such as malaria screening for elimination, diagnostic assay can be a challenge, as both the throughput and cost of the assay must be considered. The requirement of nucleic acid extraction hampers the throughput of most molecular assays. Co-amplification of multiple species or multiplex identification either can result in missed diagnosis or are too costly for large-scale screening. A genus- and species-specific diagnostic assay with simplified procedure, high sensitivity and throughput is still needed. This study aimed to develop a sensitive and high-throughput approach for large-scale infectious disease screening. Methods We developed multi-section Capture and Ligation Probe PCR (mCLIP-PCR) for the direct detection of RNA without extraction and reverse transcription. Multiple tailed sandwich hybridization probes were used to bind at genus- and species-specific sections of the target RNA to cooperatively capture the target onto a 96-well plate. After enzymatic ligation of the bound probes, a single-stranded DNA formed at each section with distinct tail sequence at the ends. They were separately PCR-amplified with primers corresponding to tail sequences for genus or species identification. We applied the method to the active screening of Plasmodium infections of 4,580 asymptomatic dried blood spot samples collected in malaria endemic areas and compared the results with standard qPCR using linear regression. Results With multi-section cooperative capture but separate amplification strategy, we accurately identified genus Plasmodium and species P. falciparum and P. vivax without RNA extraction, with favorable sensitivities among the published reports. In the active screening, our method identified all 53 positive infections including two mixed infections, and two P. vivax infections that were missed by standard qPCR. Conclusions mCLIP-PCR provides a sensitive and high-throughput approach to large-scale infectious disease screening with low cost and labor, making it a valuable tool for malaria elimination in endemic region. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s40249-022-00948-2.
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Mirahmadi H, Shahrakipour A, Mehravaran A, Rahmati-Balaghaleh M, Zarean M, Etemadi S, Shahraki M, Solgi R. Evaluation of Multiplex/Nested Polymerase Chain Reaction and Loop-Mediated Isothermal Amplification for Malaria Diagnosis in Southeastern Iran. Am J Trop Med Hyg 2022; 106:841-845. [PMID: 35100562 PMCID: PMC8922511 DOI: 10.4269/ajtmh.21-0970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/15/2021] [Indexed: 11/07/2022] Open
Abstract
Malaria is one of the most serious health problems in many countries, including Iran. Accurate diagnosis is important regardless of the elimination status of a country. A cross-sectional study was performed on 105 people who were suspected to be positive for malaria infection in Sistan and Baluchistan, Iran. Blood smears (thin and thick films) were stained with 10% Giemsa. DNA was extracted from the prepared thin and thick films for molecular methods. Multiplex/nested polymerase chain reaction (mn-PCR), loop-mediated isothermal amplification (LAMP), and light microscopy (LM) were compared with nested PCR (nPCR) as a gold standard. Of 105 subjects, 52 (49.5%), 58 (55.2%), 58 (55.2%), and 63 (60%) were positive for malaria by LM, nPCR, mn-PCR, and LAMP, respectively. The sensitivity, specificity, and kappa were 92.1%, 100%, and 0.9 for LAMP and 100%, 100%, and 1 for mn-PCR, respectively. Eight cases of coinfection (Plasmodium vivax and Plasmodium falciparum) that were not detected by LM method were diagnosed by mn-PCR and LAMP. In the present study, the high sensitivity and specificity of LAMP and mn-PCR indicate that these two tests are good alternatives to nPCR for malaria diagnosis.
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Affiliation(s)
- Hadi Mirahmadi
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran;,Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Azam Shahrakipour
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran;,Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ahmad Mehravaran
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran;,Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mansour Rahmati-Balaghaleh
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran;,Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mehdi Zarean
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran;,Cutaneous Leishmaniasis Research Center, Mashhad University of Medical Sciences, Mashhad, Iran;,Address correspondence to Rahmat Solgi, Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran, E-mail: or Mehdi Zarean, Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran, E-mail:
| | - Soodabeh Etemadi
- Infectious Diseases and Tropical Medicine Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran;,Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mehdi Shahraki
- Department of Parasitology and Mycology, Faculty of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Rahmat Solgi
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran;,Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran,Address correspondence to Rahmat Solgi, Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran, E-mail: or Mehdi Zarean, Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran, E-mail:
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Gumbo A, Topazian HM, Mwanza A, Mitchell CL, Puerto-Meredith S, Njiko R, Kayange M, Mwalilino D, Mvula B, Tegha G, Mvalo T, Hoffman I, Juliano JJ. Occurrence and Distribution of Nonfalciparum Malaria Parasite Species Among Adolescents and Adults in Malawi. J Infect Dis 2022; 225:257-268. [PMID: 34244739 PMCID: PMC8763954 DOI: 10.1093/infdis/jiab353] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/08/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Plasmodium falciparum malaria dominates throughout sub-Saharan Africa, but the prevalence of Plasmodium malariae, Plasmodium ovale spp., and Plasmodium vivax increasingly contribute to infection in countries that control malaria using P. falciparum-specific diagnostic and treatment strategies. METHODS We performed quantitative polymerase chain reaction (qPCR) on 2987 dried blood spots from the 2015-2016 Malawi Demographic and Health Survey to identify presence and distribution of nonfalciparum infection. Bivariate models were used to determine species-specific associations with demographic and environmental risk factors. RESULTS Nonfalciparum infections had broad spatial distributions. Weighted prevalence was 0.025 (SE, 0.004) for P. malariae, 0.097 (SE, 0.008) for P. ovale spp., and 0.001 (SE, 0.0005) for P. vivax. Most infections (85.6%) had low-density parasitemias ≤ 10 parasites/µL, and 66.7% of P. malariae, 34.6% of P. ovale spp., and 40.0% of P. vivax infections were coinfected with P. falciparum. Risk factors for P. malariae were like those known for P. falciparum; however, there were few risk factors recognized for P. ovale spp. and P. vivax, perhaps due to the potential for relapsing episodes. CONCLUSIONS The prevalence of any nonfalciparum infection was 11.7%, with infections distributed across Malawi. Continued monitoring of Plasmodium spp. becomes critical as nonfalciparum infections become important sources of ongoing transmission.
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Affiliation(s)
- Austin Gumbo
- National Malaria Control Programme, Malawi Ministry of Health, Lilongwe, Malawi
| | - Hillary M Topazian
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alexis Mwanza
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Cedar L Mitchell
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sydney Puerto-Meredith
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ruth Njiko
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Michael Kayange
- National Malaria Control Programme, Malawi Ministry of Health, Lilongwe, Malawi
| | - David Mwalilino
- National HIV Reference Laboratory, Malawi Ministry of Health, Lilongwe, Malawi
| | - Bernard Mvula
- National HIV Reference Laboratory, Malawi Ministry of Health, Lilongwe, Malawi
| | - Gerald Tegha
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Tisungane Mvalo
- University of North Carolina Project-Malawi, Lilongwe, Malawi
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Irving Hoffman
- University of North Carolina Project-Malawi, Lilongwe, Malawi
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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Calderaro A, Montecchini S, Buttrini M, Piccolo G, Rossi S, Arcangeletti MC, Farina B, De Conto F, Chezzi C. Malaria Diagnosis in Non-Endemic Settings: The European Experience in the Last 22 Years. Microorganisms 2021; 9:microorganisms9112265. [PMID: 34835391 PMCID: PMC8620059 DOI: 10.3390/microorganisms9112265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Accurate, prompt, and reliable tools for the diagnosis of malaria are crucial for tracking the successes or drawbacks of control and elimination efforts, and for future programs aimed at global malaria eradication. Although microscopy remains the gold standard method, the number of imported malaria cases and the risk of reappearance of autochthonous cases stimulated several laboratories located in European countries to evaluate methods and algorithms suited to non-endemic settings, where skilled microscopists are not always available. In this review, an overview of the field evaluation and a comparison of the methods used for the diagnosis of malaria by European laboratories is reported, showing that the development of numerous innovations is continuous. In particular, the combination of rapid diagnostic tests and molecular assays with microscopy represents a reliable system for the early diagnosis of malaria in non-endemic settings.
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Affiliation(s)
- Adriana Calderaro
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (S.M.); (M.B.); (G.P.); (M.C.A.); (B.F.); (F.D.C.); (C.C.)
- Correspondence: ; Tel.: +39-0521-033499; Fax: +39-0521-993620
| | - Sara Montecchini
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (S.M.); (M.B.); (G.P.); (M.C.A.); (B.F.); (F.D.C.); (C.C.)
| | - Mirko Buttrini
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (S.M.); (M.B.); (G.P.); (M.C.A.); (B.F.); (F.D.C.); (C.C.)
| | - Giovanna Piccolo
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (S.M.); (M.B.); (G.P.); (M.C.A.); (B.F.); (F.D.C.); (C.C.)
| | - Sabina Rossi
- Unit of Clinical Microbiology, University Hospital of Parma, Viale A. Gramsci 14, 43126 Parma, Italy;
| | - Maria Cristina Arcangeletti
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (S.M.); (M.B.); (G.P.); (M.C.A.); (B.F.); (F.D.C.); (C.C.)
| | - Benedetta Farina
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (S.M.); (M.B.); (G.P.); (M.C.A.); (B.F.); (F.D.C.); (C.C.)
| | - Flora De Conto
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (S.M.); (M.B.); (G.P.); (M.C.A.); (B.F.); (F.D.C.); (C.C.)
| | - Carlo Chezzi
- Department of Medicine and Surgery, University of Parma, Viale A. Gramsci 14, 43126 Parma, Italy; (S.M.); (M.B.); (G.P.); (M.C.A.); (B.F.); (F.D.C.); (C.C.)
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Amoah B, McCann RS, Kabaghe AN, Mburu M, Chipeta MG, Moraga P, Gowelo S, Tizifa T, van den Berg H, Mzilahowa T, Takken W, van Vugt M, Phiri KS, Diggle PJ, Terlouw DJ, Giorgi E. Identifying Plasmodium falciparum transmission patterns through parasite prevalence and entomological inoculation rate. eLife 2021; 10:65682. [PMID: 34672946 PMCID: PMC8530514 DOI: 10.7554/elife.65682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background Monitoring malaria transmission is a critical component of efforts to achieve targets for elimination and eradication. Two commonly monitored metrics of transmission intensity are parasite prevalence (PR) and the entomological inoculation rate (EIR). Comparing the spatial and temporal variations in the PR and EIR of a given geographical region and modelling the relationship between the two metrics may provide a fuller picture of the malaria epidemiology of the region to inform control activities. Methods Using geostatistical methods, we compare the spatial and temporal patterns of Plasmodium falciparum EIR and PR using data collected over 38 months in a rural area of Malawi. We then quantify the relationship between EIR and PR by using empirical and mechanistic statistical models. Results Hotspots identified through the EIR and PR partly overlapped during high transmission seasons but not during low transmission seasons. The estimated relationship showed a 1-month delayed effect of EIR on PR such that at lower levels of EIR, increases in EIR are associated with rapid rise in PR, whereas at higher levels of EIR, changes in EIR do not translate into notable changes in PR. Conclusions Our study emphasises the need for integrated malaria control strategies that combine vector and human host managements monitored by both entomological and parasitaemia indices. Funding This work was supported by Stichting Dioraphte grant number 13050800.
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Affiliation(s)
- Benjamin Amoah
- Centre for Health Informatics, Computing, and Statistics (CHICAS), Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
| | - Robert S McCann
- Laboratory of Entomology, Wageningen University and Research, Wageningen, Netherlands.,Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi.,Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, United States
| | - Alinune N Kabaghe
- Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi.,Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Monicah Mburu
- Laboratory of Entomology, Wageningen University and Research, Wageningen, Netherlands.,Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Michael G Chipeta
- Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi.,Malawi-Liverpool Wellcome Trust Research Programme, Blantyre, Malawi.,Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Paula Moraga
- Centre for Health Informatics, Computing, and Statistics (CHICAS), Lancaster Medical School, Lancaster University, Lancaster, United Kingdom.,Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Steven Gowelo
- Laboratory of Entomology, Wageningen University and Research, Wageningen, Netherlands.,Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Tinashe Tizifa
- Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi.,Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Henk van den Berg
- Laboratory of Entomology, Wageningen University and Research, Wageningen, Netherlands
| | - Themba Mzilahowa
- Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Willem Takken
- Laboratory of Entomology, Wageningen University and Research, Wageningen, Netherlands
| | - Michele van Vugt
- Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Kamija S Phiri
- Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Peter J Diggle
- Centre for Health Informatics, Computing, and Statistics (CHICAS), Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
| | - Dianne J Terlouw
- Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi.,Malawi-Liverpool Wellcome Trust Research Programme, Blantyre, Malawi.,Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Emanuele Giorgi
- Centre for Health Informatics, Computing, and Statistics (CHICAS), Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
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Grigg MJ, Lubis IN, Tetteh KKA, Barber BE, William T, Rajahram GS, Tan AF, Sutherland CJ, Noviyanti R, Drakeley CJ, Britton S, Anstey NM. Plasmodium knowlesi detection methods for human infections-Diagnosis and surveillance. ADVANCES IN PARASITOLOGY 2021; 113:77-130. [PMID: 34620386 DOI: 10.1016/bs.apar.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Within the overlapping geographical ranges of P. knowlesi monkey hosts and vectors in Southeast Asia, an estimated 1.5 billion people are considered at risk of infection. P. knowlesi can cause severe disease and death, the latter associated with delayed treatment occurring from misdiagnosis. Although microscopy is a sufficiently sensitive first-line tool for P. knowlesi detection for most low-level symptomatic infections, misdiagnosis as other Plasmodium species is common, and the majority of asymptomatic infections remain undetected. Current point-of-care rapid diagnostic tests demonstrate insufficient sensitivity and poor specificity for differentiating P. knowlesi from other Plasmodium species. Molecular tools including nested, real-time, and single-step PCR, and loop-mediated isothermal amplification (LAMP), are sensitive for P. knowlesi detection. However, higher cost and inability to provide the timely point-of-care diagnosis needed to guide appropriate clinical management has limited their routine use in most endemic clinical settings. P. knowlesi is likely underdiagnosed across the region, and improved diagnostic and surveillance tools are required. Reference laboratory molecular testing of malaria cases for both zoonotic and non-zoonotic Plasmodium species needs to be more widely implemented by National Malaria Control Programs across Southeast Asia to accurately identify the burden of zoonotic malaria and more precisely monitor the success of human-only malaria elimination programs. The implementation of specific serological tools for P. knowlesi would assist in determining the prevalence and distribution of asymptomatic and submicroscopic infections, the absence of transmission in certain areas, and associations with underlying land use change for future spatially targeted interventions.
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Affiliation(s)
- Matthew J Grigg
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia.
| | - Inke N Lubis
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Sumatera Utara, Indonesia
| | - Kevin K A Tetteh
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bridget E Barber
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia; QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia; Clinical Research Centre, Queen Elizabeth Hospital 1, Kota Kinabalu, Malaysia; Gleneagles Medical Centre, Kota Kinabalu, Malaysia
| | - Giri S Rajahram
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia; Clinical Research Centre, Queen Elizabeth Hospital 1, Kota Kinabalu, Malaysia; Queen Elizabeth Hospital 2, Kota Kinabalu, Malaysia
| | - Angelica F Tan
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
| | - Colin J Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Chris J Drakeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sumudu Britton
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicholas M Anstey
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Kota Kinabalu, Sabah, Malaysia
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Zhang C, Yang R, Wu L, Luo C, Guo X, Deng Y, Zhou H, Zhang Y. Molecular phylogeny of the Anopheles hyrcanus group (Diptera: Culicidae) based on rDNA-ITS2 and mtDNA-COII. Parasit Vectors 2021; 14:454. [PMID: 34488860 PMCID: PMC8420049 DOI: 10.1186/s13071-021-04971-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Anopheles hyrcanus group, which includes 25 species, is widely distributed in the Oriental and Palaearctic regions. Given the difficulty in identifying cryptic or sibling species based on their morphological characteristics, molecular identification is regarded as an important complementary approach to traditional morphological taxonomy. The aim of this study was to reconstruct the phylogeny of the Hyrcanus group using DNA barcoding markers in order to determine the phylogenetic correlations of closely related taxa and to compare these markers in terms of identification efficiency and genetic divergence among species. METHODS Based on data extracted from the GenBank database and data from the present study, we used 399 rDNA-ITS2 sequences of 19 species and 392 mtDNA-COII sequences of 14 species to reconstruct the molecular phylogeny of the Hyrcanus group across its worldwide range. We also compared the performance of rDNA-ITS2 against that of mtDNA-COII to assess the genetic divergence of closely related species within the Hyrcanus group. RESULTS Average interspecific divergence for the rDNA-ITS2 sequence (0.376) was 125-fold higher than the average intraspecies divergence (0.003), and average interspecific divergence for the mtDNA-COII sequence (0.055) was eightfold higher than the average intraspecies divergence (0.007). The barcoding gap ranged from 0.015 to 0.073 for rDNA-ITS2, and from 0.017 to 0.025 for mtDNA-COII. Two sets of closely related species, namely, Anophels lesteri and An. paraliae, and An. sinensis, An. belenrae and An. kleini, were resolved by rDNA-ITS2. In contrast, the relationship of An. sinensis/An. belenrae/An. kleini was poorly defined in the COII tree. The neutrality test and mismatch distribution revealed that An. peditaeniatus, An. hyrcanus, An. sinensis and An. lesteri were likely to undergo hitchhiking or population expansion in accordance with both markers. In addition, the population of an important vivax malaria vector, An. sinensis, has experienced an expansion after a bottleneck in northern and southern Laos. CONCLUSIONS The topology of the Hyrcanus group rDNA-ITS2 and mtDNA-COII trees conformed to the morphology-based taxonomy for species classification rather than for that for subgroup division. rDNA-ITS2 is considered to be a more reliable diagnostic tool than mtDNA-COII in terms of investigating the phylogenetic correlation between closely related mosquito species in the Hyrcanus group. Moreover, the population expansion of an important vivax malaria vector, An. sinensis, has underlined a potential risk of malaria transmission in northern and southern Laos. This study contributes to the molecular identification of the Anopheles hyrcanus group in vector surveillance.
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Affiliation(s)
- Canglin Zhang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Rui Yang
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Linbo Wu
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Chunhai Luo
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Xiaofang Guo
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Yan Deng
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Hongning Zhou
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Yunnan Provincial Collaborative Innovation Center for Public Health and Disease Prevention and Control, Yunnan Institute of Parasitic Diseases Innovative Team of Key Techniques for Vector Borne Disease Control and Prevention (Developing), Yunnan Institute of Parasitic Diseases, Pu’er, 665099 People’s Republic of China
| | - Yilong Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433 People’s Republic of China
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Mburu MM, Zembere K, Mzilahowa T, Terlouw AD, Malenga T, van den Berg H, Takken W, McCann RS. Impact of cattle on the abundance of indoor and outdoor resting malaria vectors in southern Malawi. Malar J 2021; 20:353. [PMID: 34446033 PMCID: PMC8390081 DOI: 10.1186/s12936-021-03885-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/16/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Understanding the blood feeding preferences and resting habits of malaria vectors is important for assessing and designing effective malaria vector control tools. The presence of livestock, such as cattle, which are used as blood meal hosts by some malaria vectors, may impact malaria parasite transmission dynamics. The presence of livestock may provide sufficient blood meals for the vectors, thereby reducing the frequency of vectors biting humans. Alternatively, the presence of cattle may enhance the availability of blood meals such that infectious mosquitoes may survive longer, thereby increasing the risk of malaria transmission. This study assessed the effect of household-level cattle presence and distribution on the abundance of indoor and outdoor resting malaria vectors. METHODS Houses with and without cattle were selected in Chikwawa district, southern Malawi for sampling resting malaria vectors. Prokopack aspirators and clay pots were used for indoor and outdoor sampling, respectively. Each house was sampled over two consecutive days. For houses with cattle nearby, the number of cattle and the distances from the house to where the cattle were corralled the previous night were recorded. All data were analysed using generalized linear models fitted with Poisson distribution. RESULTS The malaria vectors caught resting indoors were Anopheles gambiae sensu stricto (s.s.), Anopheles arabiensis and Anopheles funestus s.s. Outdoor collections consisted primarily of An. arabiensis. The catch sizes of indoor resting An. gambiae sensu lato (s.l.) were not different in houses with and without cattle (P = 0.34). The presence of cattle near a house was associated with a reduction in the abundance of indoor resting An. funestus s.l. (P = 0.04). This effect was strongest when cattle were kept overnight ≤ 15 m away from the houses (P = 0.03). The blood meal hosts varied across the species. CONCLUSION These results highlight differences between malaria vector species and their interactions with potential blood meal hosts, which may have implications for malaria risk. Whereas An. arabiensis remained unaffected, the reduction of An. funestus s.s. in houses near cattle suggests a potential protective effect of cattle. However, the low abundance of mosquitoes reduced the power of some analyses and limited the generalizability of the results to other settings. Therefore, further studies incorporating the vectors' host-seeking behaviour/human biting rates are recommended to fully support the primary finding.
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Affiliation(s)
- Monicah M Mburu
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi.
- Laboratory of Entomology, Wageningen University and Research, Wageningen, The Netherlands.
- Macha Research Trust, Choma, Zambia.
| | - Kennedy Zembere
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
- Malawi-Liverpool-Wellcome Trust, Blantyre, Malawi
| | - Themba Mzilahowa
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
- MAC Communicable Diseases Action Centre, Blantyre, Malawi
| | - Anja D Terlouw
- Malawi-Liverpool-Wellcome Trust, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Tumaini Malenga
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Henk van den Berg
- Laboratory of Entomology, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem Takken
- Laboratory of Entomology, Wageningen University and Research, Wageningen, The Netherlands
| | - Robert S McCann
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
- Laboratory of Entomology, Wageningen University and Research, Wageningen, The Netherlands
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, USA
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Christensen P, Bozdech Z, Watthanaworawit W, Imwong M, Rénia L, Malleret B, Ling C, Nosten F. Reverse transcription PCR to detect low density malaria infections. Wellcome Open Res 2021; 6:39. [PMID: 35592834 PMCID: PMC9086519 DOI: 10.12688/wellcomeopenres.16564.2] [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] [Accepted: 07/29/2021] [Indexed: 05/14/2024] Open
Abstract
Background: Targeted malaria elimination strategies require highly sensitive tests to detect low density malaria infections (LDMI). Commonly used methods for malaria diagnosis such as light microscopy and antigen-based rapid diagnostic tests (RDTs) are not sensitive enough for reliable identification of infections with parasitaemia below 200 parasites per milliliter of blood. While targeted malaria elimination efforts on the Thailand-Myanmar border have successfully used high sample volume ultrasensitive quantitative PCR (uPCR) to determine malaria prevalence, the necessity for venous collection and processing of large quantities of patient blood limits the widespread tractability of this method. Methods: Here we evaluated a real-time reverse transcription PCR (RT-qPCR) method that reduces the required sample volume compared to uPCR. To do this, 304 samples collected from an active case detection program in Kayin state, Myanmar were compared using uPCR and RT-qPCR. Results: Plasmodium spp. RT-qPCR confirmed 18 of 21 uPCR Plasmodium falciparum positives, while P. falciparum specific RT-qPCR confirmed 17 of the 21 uPCR P. falciparum positives. Combining both RT-qPCR results increased the sensitivity to 100% and specificity was 95.1%. Conclusion: Malaria detection in areas of low transmission and LDMI can benefit from the increased sensitivity of ribosomal RNA detection by RT-PCR, especially where sample volume is limited. Isolation of high quality RNA also allows for downstream analysis of malaria transcripts.
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Affiliation(s)
- Peter Christensen
- Shoklo Malaria Research Unit, Mahidol University, Maesot, Tak, 63110, Thailand
- Microbiology and Immunology, University of Otago, Dunedin, Otago, 9016, New Zealand
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Laurent Rénia
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
- A*STAR ID Labs, A*STAR, Singapore, 138648, Singapore
| | - Benoît Malleret
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
- Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Clare Ling
- Shoklo Malaria Research Unit, Mahidol University, Maesot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol University, Maesot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Gimenez AM, Marques RF, Regiart M, Bargieri DY. Diagnostic Methods for Non-Falciparum Malaria. Front Cell Infect Microbiol 2021; 11:681063. [PMID: 34222049 PMCID: PMC8248680 DOI: 10.3389/fcimb.2021.681063] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Malaria is a serious public health problem that affects mostly the poorest countries in the world, killing more than 400,000 people per year, mainly children under 5 years old. Among the control and prevention strategies, the differential diagnosis of the Plasmodium-infecting species is an important factor for selecting a treatment and, consequently, for preventing the spread of the disease. One of the main difficulties for the detection of a specific Plasmodium sp is that most of the existing methods for malaria diagnosis focus on detecting P. falciparum. Thus, in many cases, the diagnostic methods neglect the other non-falciparum species and underestimate their prevalence and severity. Traditional methods for diagnosing malaria may present low specificity or sensitivity to non-falciparum spp. Therefore, there is high demand for new alternative methods able to differentiate Plasmodium species in a faster, cheaper and easier manner to execute. This review details the classical procedures and new perspectives of diagnostic methods for malaria non-falciparum differential detection and the possibilities of their application in different circumstances.
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Affiliation(s)
- Alba Marina Gimenez
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rodolfo F. Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Matías Regiart
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Daniel Youssef Bargieri
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Schneider R, Lamien-Meda A, Auer H, Wiedermann-Schmidt U, Chiodini PL, Walochnik J. Validation of a novel FRET real-time PCR assay for simultaneous quantitative detection and discrimination of human Plasmodium parasites. PLoS One 2021; 16:e0252887. [PMID: 34086817 PMCID: PMC8177637 DOI: 10.1371/journal.pone.0252887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/25/2021] [Indexed: 11/19/2022] Open
Abstract
Increasing numbers of travelers returning from endemic areas, migrants, and refugees have led to a significant rise in the number of imported malaria cases in non-endemic countries. Real- time PCR serves as an excellent diagnostic tool, especially in regions where experience in microscopy is limited. A novel fluorescence resonance energy transfer-based real-time PCR (FRET-qPCR) was developed and evaluated using 56 reference samples of the United Kingdom National External Quality Assessment Service (UK NEQAS) for molecular detection of malaria, including P. falciparum, P. vivax, P. ovale, P. malariae, and P. knowlesi. Species identification is based on single nucleotide polymorphisms (SNPs) within the genome where the MalLC640 probe binds, lowering the melting temperature in the melting curve analysis. The novel FRET-qPCR achieved 100% (n = 56) correct results, compared to 96.43% performing nested PCR. The high sensitivity, with a calculated limit of detection of 199.97 parasites/mL blood for P. falciparum, is a significant advantage, especially if low-level parasitemia has to be ruled out. Even mixed infections of P. falciparum with P. vivax or P. ovale, respectively, were detected. In contrast to many other real-time PCR protocols, this novel FRET-qPCR allows the quantitative and species-specific detection of Plasmodium spp. in one single run. Solely, P. knowlesi was detected but could not be differentiated from P. vivax. The turnaround time of this novel FRET-qPCR including DNA extraction is less than two hours, qualifying it for routine clinical applications, including treatment monitoring.
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Affiliation(s)
- Renate Schneider
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Aline Lamien-Meda
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Herbert Auer
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Ursula Wiedermann-Schmidt
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Peter L. Chiodini
- UK NEQAS Parasitology, Public Health England, London, United Kingdom
| | - Julia Walochnik
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
- * E-mail:
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Cunningham CH, Hennelly CM, Lin JT, Ubalee R, Boyce RM, Mulogo EM, Hathaway N, Thwai KL, Phanzu F, Kalonji A, Mwandagalirwa K, Tshefu A, Juliano JJ, Parr JB. A novel CRISPR-based malaria diagnostic capable of Plasmodium detection, species differentiation, and drug-resistance genotyping. EBioMedicine 2021; 68:103415. [PMID: 34139428 PMCID: PMC8213918 DOI: 10.1016/j.ebiom.2021.103415] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND CRISPR-based diagnostics are a new class of highly sensitive and specific assays with multiple applications in infectious disease diagnosis. SHERLOCK, or Specific High-Sensitivity Enzymatic Reporter UnLOCKing, is one such CRISPR-based diagnostic that combines recombinase polymerase pre-amplification, CRISPR-RNA base-pairing, and LwCas13a activity for nucleic acid detection. METHODS We developed SHERLOCK assays capable of detecting all Plasmodium species known to cause human malaria and species-specific detection of P. vivax and P. falciparum, the species responsible for the majority of malaria cases worldwide. We further tested these assays using a diverse panel of clinical samples from the Democratic Republic of the Congo, Uganda, and Thailand and pools of Anopheles mosquitoes from Thailand. In addition, we developed a prototype SHERLOCK assay capable of detecting the dihydropteroate synthetase (dhps) single nucleotide variant A581G associated with P. falciparum sulfadoxine resistance. FINDINGS The suite of Plasmodium assays achieved analytical sensitivities ranging from 2•5-18•8 parasites per reaction when tested against laboratory strain genomic DNA. When compared to real-time PCR, the P. falciparum assay achieved 94% sensitivity and 94% specificity during testing of 123 clinical samples. Compared to amplicon-based deep sequencing, the dhps SHERLOCK assay achieved 73% sensitivity and 100% specificity when applied to a panel of 43 clinical samples, with false-negative calls only at lower parasite densities. INTERPRETATION These novel SHERLOCK assays demonstrate the versatility of CRISPR-based diagnostics and their potential as a new generation of molecular tools for malaria diagnosis and surveillance. FUNDING National Institutes of Health (T32GM007092, R21AI148579, K24AI134990, R01AI121558, UL1TR002489, P30CA016086).
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Affiliation(s)
- Clark H Cunningham
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - Jessica T Lin
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ratawan Ubalee
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Ross M Boyce
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Mbarara University of Science and Technology, Mbarara, Uganda
| | - Edgar M Mulogo
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Nicholas Hathaway
- University of Massachusetts School of Medicine, Worcester, MA, United States
| | - Kyaw L Thwai
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Fernandine Phanzu
- SANRU ASBL (Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Albert Kalonji
- SANRU ASBL (Global Fund), Kinshasa, Democratic Republic of the Congo
| | | | - Antoinette Tshefu
- Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo
| | - Jonathan J Juliano
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jonathan B Parr
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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Liu S, Huckaby AC, Brown AC, Moore CC, Burbulis I, McConnell MJ, Güler JL. Single-cell sequencing of the small and AT-skewed genome of malaria parasites. Genome Med 2021; 13:75. [PMID: 33947449 PMCID: PMC8094492 DOI: 10.1186/s13073-021-00889-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/17/2021] [Indexed: 12/23/2022] Open
Abstract
Single-cell genomics is a rapidly advancing field; however, most techniques are designed for mammalian cells. We present a single-cell sequencing pipeline for an intracellular parasite, Plasmodium falciparum, with a small genome of extreme base content. Through optimization of a quasi-linear amplification method, we target the parasite genome over contaminants and generate coverage levels allowing detection of minor genetic variants. This work, as well as efforts that build on these findings, will enable detection of parasite heterogeneity contributing to P. falciparum adaptation. Furthermore, this study provides a framework for optimizing single-cell amplification and variant analysis in challenging genomes.
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Affiliation(s)
- Shiwei Liu
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Adam C Huckaby
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Audrey C Brown
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Christopher C Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Ian Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
- Current address: Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Jennifer L Güler
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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Motshoge T, Haiyambo DH, Ayanful-Torgby R, Aleksenko L, Ntebela D, Malleret B, Rénia L, Peloewetse E, Paganotti GM, Quaye IK. Recent Molecular Assessment of Plasmodium vivax and Plasmodium falciparum Asymptomatic Infections in Botswana. Am J Trop Med Hyg 2021; 104:2159-2164. [PMID: 33939635 PMCID: PMC8176517 DOI: 10.4269/ajtmh.21-0083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/09/2021] [Indexed: 01/05/2023] Open
Abstract
In 2016, we reported the presence of Plasmodium vivax in Botswana through active case detection. A real-time PCR was used during a similar study in 10 districts to assess changes in the P. vivax prevalence. We assessed 1,614 children (2-13 years of age) for hemoglobin (Hb; g/dL) and Plasmodium parasites. The median age of all participants was 5.0 years (25th percentile, 3 years; 75th percentile, 8 years). The median Hb (g/dL) level was 12.1, but 18.3% of the participants had anemia (Hb < 11.0 g/dL); these participants were clustered in the younger than 5 years age group in all districts (P < 0.001). The risk of anemia decreased with age 5 years or older (odds ratio [OR], 0.26; 95% confidence interval [CI], 0.197-0.34; P < 0.001). The prevalence rates of Plasmodium parasites were as follows: P. vivax, 12.7%; P. falciparum, 12.7%; P. malariae, 0.74%; and P. ovale (P. ovale curtisi), 0.68%. Mixed infection rates were as follows: P. falciparum and P. vivax, 2.35%; P. falciparum and P. ovale curtisi, 0.56%; P. vivax and P. malariae, 0.06%; and P. falciparum and P. malariae, 0.68%. The infections were largely asymptomatic (99.6%). Using logistic regression, the risk of infection with P. vivax was highest in Kweneng East (OR, 6.2; 95% CI, 2.9-13.1), followed by South East (OR, 5.6; 95% CI, 2.5-12.3) and Ngami (OR, 5.1; 95% CI, 2.2-12.0). Compared to the risk of infection for children younger than 5 years, the risk of infection decreased for children 5 years or older in regions with high rates of P. vivax and P. falciparum infections. P. vivax and P. falciparum have expanded within the asymptomatic population in Botswana; therefore, careful attention is required for their elimination.
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Affiliation(s)
- Thato Motshoge
- University of Botswana, Department of Biological Science, Gaborone, Botswana
| | | | - Ruth Ayanful-Torgby
- Regent University College of Science and Technology, Department of Engineering, Computing and Allied Health Sciences, Accra, Ghana
- Biomedical and Public Health Research Unit, Council for Scientific and Industrial Research–Water Research Institute, Council Close, Accra, Ghana
| | | | - Davies Ntebela
- National Malaria Program Ministry of Health and Wellness, Gaborone, Botswana
| | - Benoit Malleret
- Department of Microbiology and Immunology, Immunology Translational Research Program, Yong Loo Lin School of Medicine, Immunology Program, Life Sciences Institute, National University of Singapore, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
| | - Laurent Rénia
- A*STAR Infectious Diseases Laboratories, Agency for Science, Technology and Research (A*STAR), Biopolis, Singapore
| | - Elias Peloewetse
- University of Botswana, Department of Biological Science, Gaborone, Botswana
| | - Giacomo Maria Paganotti
- Botswana–University of Pennsylvania Partnership, University of Botswana, Gaborone, Botswana
- Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Isaac K. Quaye
- Regent University College of Science and Technology, Department of Engineering, Computing and Allied Health Sciences, Accra, Ghana
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Sazed SA, Kibria MG, Alam MS. An Optimized Real-Time qPCR Method for the Effective Detection of Human Malaria Infections. Diagnostics (Basel) 2021; 11:736. [PMID: 33919020 PMCID: PMC8142979 DOI: 10.3390/diagnostics11050736] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/24/2022] Open
Abstract
Polymerase chain reaction, although an expensive method for the detection of human Plasmodium spp., is still considered the finest for the diagnosis of malaria. The conventional diagnostic PCR is an inexpensive process but consumes a lot of time, reagents and lacks sensitivity. On the other hand, real-time PCR assays currently being used are mostly probe-based expensive methods and sometimes not feasible to detect all the species in a single amplification reaction condition. Here we have established a real-time PCR method that is time and cost effective with a single protocol to detect and distinguish five human Plasmodium species using the existing primers efficiently. The primers used here are being used in the conventional method and the sensitivity as well as specificity of this method has also been immensely improved (100%). The lower limit of detection for Plasmodium falciparum, Plasmodium vivax and Plasmodium malariae are 0.064 parasites/µL, 1.6 parasites/µL, and 0.32 parasites/µL respectively and no cross reactivity was observed. Besides, we have analyzed melt curves that can be used for further species confirmation and validation purposes using multiplex systems. This method, therefore, can be considered as an alternative to the existing lineup for molecular diagnosis of malaria in endemic countries.
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Affiliation(s)
| | | | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh Mohakhali, Dhaka 1212, Bangladesh; (S.A.S.); (M.G.K.)
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Parr JB, Kieto E, Phanzu F, Mansiangi P, Mwandagalirwa K, Mvuama N, Landela A, Atibu J, Efundu SU, Olenga JW, Thwai KL, Morgan CE, Denton M, Poffley A, Juliano JJ, Mungala P, Likwela JL, Sompwe EM, Rogier E, Tshefu AK, N'Siala A, Kalonji A. Analysis of false-negative rapid diagnostic tests for symptomatic malaria in the Democratic Republic of the Congo. Sci Rep 2021; 11:6495. [PMID: 33753817 PMCID: PMC7985209 DOI: 10.1038/s41598-021-85913-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/08/2021] [Indexed: 11/29/2022] Open
Abstract
The majority of Plasmodium falciparum malaria diagnoses in Africa are made using rapid diagnostic tests (RDTs) that detect histidine-rich protein 2. Increasing reports of false-negative RDT results due to parasites with deletions of the pfhrp2 and/or pfhrp3 genes (pfhrp2/3) raise concern about existing malaria diagnostic strategies. We previously identified pfhrp2-negative parasites among asymptomatic children in the Democratic Republic of the Congo (DRC), but their impact on diagnosis of symptomatic malaria is unknown. We performed a cross-sectional study of false-negative RDTs in symptomatic subjects in 2017. Parasites were characterized by microscopy; RDT; pfhrp2/3 genotyping and species-specific PCR assays; a bead-based immunoassay for Plasmodium antigens; and/or whole-genome sequencing. Among 3627 symptomatic subjects, 427 (11.8%) had RDT-/microscopy + results. Parasites from eight (0.2%) samples were initially classified as putative pfhrp2/3 deletions by PCR, but antigen testing and whole-genome sequencing confirmed the presence of intact genes. 56.8% of subjects had PCR-confirmed malaria. Non-falciparum co-infection with P. falciparum was common (13.2%). Agreement between PCR and HRP2-based RDTs was satisfactory (Cohen's kappa = 0.66) and superior to microscopy (0.33). Symptomatic malaria due to pfhrp2/3-deleted P. falciparum was not observed. Ongoing HRP2-based RDT use is appropriate for the detection of falciparum malaria in the DRC.
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Affiliation(s)
- Jonathan B Parr
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, University of North Carolina, 130 Mason Farm Rd, Chapel Hill, NC, 27599, USA.
| | - Eddy Kieto
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Fernandine Phanzu
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Paul Mansiangi
- University of Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | | | - Nono Mvuama
- University of Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Ange Landela
- Institut National Pour La Recherche Biomedicale, Kinshasa, Democratic Republic of the Congo
| | - Joseph Atibu
- University of Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | | | - Jean W Olenga
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Kyaw Lay Thwai
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, University of North Carolina, 130 Mason Farm Rd, Chapel Hill, NC, 27599, USA
| | - Camille E Morgan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Madeline Denton
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, University of North Carolina, 130 Mason Farm Rd, Chapel Hill, NC, 27599, USA
| | - Alison Poffley
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, University of North Carolina, 130 Mason Farm Rd, Chapel Hill, NC, 27599, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Pomie Mungala
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Joris L Likwela
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Eric M Sompwe
- Programme National de La Lutte Contre Le Paludisme, Kinshasa, Democratic Republic of Congo
| | - Eric Rogier
- Malaria Branch, Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA, 30033, USA
| | - Antoinette K Tshefu
- University of Kinshasa School of Public Health, Kinshasa, Democratic Republic of Congo
| | - Adrien N'Siala
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
| | - Albert Kalonji
- SANRU Asbl (Sante Rurale/Global Fund), Kinshasa, Democratic Republic of the Congo
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Christensen P, Bozdech Z, Watthanaworawit W, Imwong M, Rénia L, Malleret B, Ling C, Nosten F. Reverse transcription PCR to detect low density malaria infections. Wellcome Open Res 2021; 6:39. [PMID: 35592834 PMCID: PMC9086519 DOI: 10.12688/wellcomeopenres.16564.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2021] [Indexed: 05/14/2024] Open
Abstract
Background: Targeted malaria elimination strategies require highly sensitive tests to detect low density malaria infections (LDMI). Commonly used methods for malaria diagnosis such as light microscopy and antigen-based rapid diagnostic tests (RDTs) are not sensitive enough for reliable identification of infections with parasitaemia below 200 parasites per milliliter of blood. While targeted malaria elimination efforts on the Thailand-Myanmar border have successfully used high sample volume ultrasensitive quantitative PCR (uPCR) to determine malaria prevalence, the necessity for venous collection and processing of large quantities of patient blood limits the widespread tractability of this method. Methods: Here we evaluated a real-time reverse transcription PCR (RT-PCR) method that reduces the required sample volume compared to uPCR. To do this, 304 samples collected from an active case detection program in Kayin state, Myanmar were compared using uPCR and RT-PCR. Results: Plasmodium spp. RT-PCR confirmed 18 of 21 uPCR Plasmodium falciparum positives, while P. falciparum specific RT-PCR confirmed 17 of the 21 uPCR P. falciparum positives. Combining both RT-PCR results increased the sensitivity to 100% and specificity was 95.1%. Conclusion: Malaria detection in areas of low transmission and LDMI can benefit from the increased sensitivity of ribosomal RNA detection by RT-PCR, especially where sample volume is limited. Isolation of high quality RNA also allows for downstream analysis of malaria transcripts.
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Affiliation(s)
- Peter Christensen
- Shoklo Malaria Research Unit, Mahidol University, Maesot, Tak, 63110, Thailand
- Microbiology and Immunology, University of Otago, Dunedin, Otago, 9016, New Zealand
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Thailand
| | - Laurent Rénia
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
- A*STAR ID Labs, A*STAR, Singapore, 138648, Singapore
| | - Benoît Malleret
- Singapore Immunology Network, A*STAR, Singapore, 138648, Singapore
- Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Clare Ling
- Shoklo Malaria Research Unit, Mahidol University, Maesot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol University, Maesot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Kolluri N, Kamath S, Lally P, Zanna M, Galagan J, Gitaka J, Kamita M, Cabodi M, Lolabattu SR, Klapperich CM. Development and Clinical Validation of Iso-IMRS: A Novel Diagnostic Assay for P. falciparum Malaria. Anal Chem 2021; 93:2097-2105. [PMID: 33464825 PMCID: PMC7859932 DOI: 10.1021/acs.analchem.0c03847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
In many countries
targeting malaria elimination, persistent malaria
infections can have parasite loads significantly below the lower limit
of detection (LLOD) of standard diagnostic techniques, making them
difficult to identify and treat. The most sensitive diagnostic methods
involve amplification and detection of Plasmodium DNA by polymerase chain reaction (PCR), which requires expensive
thermal cycling equipment and is difficult to deploy in resource-limited
settings. Isothermal DNA amplification assays have been developed,
but they require
complex primer design, resulting in high nonspecific amplification,
and show a decrease in sensitivity than PCR methods. Here, we have
used a computational approach to design a novel isothermal amplification
assay with a simple primer design to amplify P. falciparum DNA with analytical sensitivity comparable to PCR. We have identified
short DNA sequences repeated throughout the parasite genome to be
used as primers for DNA amplification and demonstrated that these
primers can be used, without modification, to isothermally amplify P. falciparum parasite DNA via strand displacement
amplification. Our novel assay shows a LLOD of ∼1 parasite/μL
within a 30 min amplification time. The assay was demonstrated with
clinical samples using patient blood and saliva. We further characterized
the assay using direct amplicon next-generation sequencing and modified
the assay to work with a visual readout. The technique developed here
achieves similar analytical sensitivity to current gold standard PCR
assays requiring a fraction of time and resources for PCR. This highly
sensitive isothermal assay can be more easily adapted to field settings,
making it a potentially useful tool for malaria elimination.
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Affiliation(s)
- Nikunja Kolluri
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Shwetha Kamath
- Division of Research and Development, Jigsaw Bio Solutions Private Limited, No. 87, 4th Floor, Mundhra Chambers, 22nd Main, Banashankari 2nd Stage, Bangalore 560070, Karnataka, India
| | - Patrick Lally
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Mina Zanna
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - James Galagan
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, General Kago Road, P.O. Box 342, Thika 01000, Kenya
| | - Moses Kamita
- Directorate of Research and Innovation, Mount Kenya University, General Kago Road, P.O. Box 342, Thika 01000, Kenya
| | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Srinivasa Raju Lolabattu
- Division of Research and Development, Jigsaw Bio Solutions Private Limited, No. 87, 4th Floor, Mundhra Chambers, 22nd Main, Banashankari 2nd Stage, Bangalore 560070, Karnataka, India
| | - Catherine M Klapperich
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
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Koliopoulos P, Kayange NM, Daniel T, Huth F, Gröndahl B, Medina-Montaño GC, Pretsch L, Klüber J, Schmidt C, Züchner A, Ulbert S, Mshana SE, Addo M, Gehring S. Multiplex-RT-PCR-ELISA panel for detecting mosquito-borne pathogens: Plasmodium sp. preserved and eluted from dried blood spots on sample cards. Malar J 2021; 20:66. [PMID: 33526038 PMCID: PMC7851927 DOI: 10.1186/s12936-021-03595-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/15/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Children are the most vulnerable group affected by malaria and other tropical, vector-borne diseases in low-resource countries. Infants presenting with acute onset fever represent a major sector of outpatient care in the Lake Victoria region. Misclassification and overuse of antibiotics and anti-malarial medications are consistent problems. Identifying the prevalent mosquito-borne pathogens in the region will reduce the prescription of non-indicated medicines. METHODS The literature was reviewed focusing on the mosquito-borne pathogens most prevalent in sub-Saharan Africa. Accordingly, an assay comprised of a multiplex-reverse transcriptase-polymerase chain reaction and an enzyme-linked immunosorbent assay (multiplex-RT-PCR-ELISA) was designed and validated in its ability to identify and differentiate nine human mosquito-borne pathogens including eight arboviruses and Plasmodium sp., the aetiologic agents of malaria. Blood samples obtained from 132 children suspected of having malaria were spotted and preserved on Whatman® 903 protein sample cards. Multiplex-RT-PCR-ELISA analysis was assessed and compared to results obtained by blood smear microscopy and the malaria rapid diagnostic test (RDT). RESULTS Nine out of nine pathogens were amplified specifically by the multiplex-RT-PCR-ELISA panel. Twenty-seven out of 132 paediatric patients presenting with acute fever were infected with Plasmodium sp., confirmed by multiplex-RT-PCR. The results of blood smear microscopy were only 40% sensitive and 92.8% specific. The malaria RDT, on the other hand, detected acute Plasmodium infections with 96.3% sensitivity and 98.1% specificity. The preservation of Plasmodium sp. in clinical sera and whole blood samples spotted on sample cards was evaluated. The duration of successful, sample card storage was 186 to 312 days. CONCLUSIONS Reliable, easy-to-use point of care diagnostic tests are a powerful alternative to laboratory-dependent gold standard tests. The multiplex-RT-PCR-ELISA amplified and identified nine vector-borne pathogens including Plasmodium sp. with great accuracy. Translation of improved diagnostic approaches, i.e., multiplex-RT-PCR-ELISA, into effective treatment options promises to reduce childhood mortality and non-indicated prescriptions.
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Affiliation(s)
- Philip Koliopoulos
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany
| | - Neema Mathias Kayange
- Department of Pediatric and Adolescent Medicine, Bugando Medical Centre, Mwanza, Tanzania
| | - Tim Daniel
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany
| | - Florian Huth
- Department of Infectiology and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Eppendorf, Germany
| | - Britta Gröndahl
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany.
| | | | - Leah Pretsch
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany
| | - Julia Klüber
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany.,Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Christian Schmidt
- Department of Pediatric and Adolescent Medicine, St. Vinzenz-Hospital, Dinslaken, Germany
| | - Antke Züchner
- Department of Pediatric and Adolescent Medicine, Bugando Medical Centre, Mwanza, Tanzania
| | - Sebastian Ulbert
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Steven E Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Marylyn Addo
- Department of Infectiology and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Eppendorf, Germany
| | - Stephan Gehring
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany
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Kotepui M, Masangkay FR, Kotepui KU, De Jesus Milanez G. Misidentification of Plasmodium ovale as Plasmodium vivax malaria by a microscopic method: a meta-analysis of confirmed P. ovale cases. Sci Rep 2020; 10:21807. [PMID: 33311528 PMCID: PMC7733466 DOI: 10.1038/s41598-020-78691-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/27/2020] [Indexed: 12/22/2022] Open
Abstract
Plasmodium ovale is a benign tertian malaria parasite that morphologically resembles Plasmodium vivax. P. ovale also shares similar tertian periodicity and can cause relapse in patients without a radical cure, making it easily misidentified as P. vivax in routine diagnosis. Therefore, its prevalence might be underreported worldwide. The present study aimed to quantify the prevalence of P. ovale misidentified as P. vivax malaria using data from studies reporting confirmed P. ovale cases by molecular methods. Studies reporting the misidentification of P. ovale as P. vivax malaria were identified from three databases, MEDLINE, Web of Science, and Scopus, without language restrictions, but the publication date was restricted to 1993 and 2020. The quality of the included studies was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS). The random-effects model was used to estimate the pooled prevalence of the misidentification of P. ovale as P. vivax malaria by the microscopic method when compared to those with the reference polymerase chain reaction method. Subgroup analysis of participants was also performed to demonstrate the difference between imported and indigenous P. ovale cases. The heterogeneity of the included studies was assessed using Cochran's Q and I2 statistics. Publication bias across the included studies was assessed using the funnel plot and Egger’s test, and if required, contour-enhanced funnel plots were used to identify the source(s) of funnel plot asymmetry. Of 641 articles retrieved from databases, 22 articles met the eligibility criteria and were included in the present study. Of the 8,297 malaria-positive cases identified by the PCR method, 453 P. ovale cases were confirmed. The pooled prevalence of misidentification of P. ovale as P. vivax malaria by the microscopic method was 11% (95% CI: 7–14%, I2: 25.46%). Subgroup analysis of the participants demonstrated a higher prevalence of misidentification in indigenous cases (13%, 95% CI: 6–21%, I2: 27.8%) than in imported cases (10%, 95% CI: 6–14%, I2: 24.1%). The pooled prevalence of misidentification of P. vivax as P. ovale malaria by the microscopic method was 1%, without heterogeneity (95% CI: 0–3%, I2: 16.8%). PCR was more sensitive in identifying P. ovale cases than the microscopic method (p < 0.00001, OR: 2.76, 95% CI: 1.83–4.15, I2: 65%). Subgroup analysis of participants demonstrated the better performance of PCR in detecting P. ovale malaria in indigenous cases (p: 0.0009, OR: 6.92, 95% CI: 2.21–21.7%, I2: 68%) than in imported cases (p: 0.0004, OR: 2.15, 95% CI: 1.41–3.29%, I2: 63%). P. ovale infections misidentified as P. vivax malaria by the microscopic method were frequent and led to underreported P. ovale cases. The molecular identification of P. ovale malaria in endemic areas is needed because a higher rate of P. ovale misidentification was found in endemic or indigenous cases than in imported cases. In addition, updated courses, enhanced training, and refreshers for microscopic examinations, particularly for P. ovale identification, are necessary to improve the microscopic identification of Plasmodium species in rural health centres where PCR is unavailable.
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Affiliation(s)
- Manas Kotepui
- Medical Technology, School of Allied Health Sciences, Walailak University, Tha Sala, Nakhon Si Thammarat, Thailand.
| | - Frederick Ramirez Masangkay
- Department of Medical Technology, Institute of Arts and Sciences, Far Eastern University-Manila, Manila, Philippines
| | - Kwuntida Uthaisar Kotepui
- Medical Technology, School of Allied Health Sciences, Walailak University, Tha Sala, Nakhon Si Thammarat, Thailand
| | - Giovanni De Jesus Milanez
- Department of Medical Technology, Institute of Arts and Sciences, Far Eastern University-Manila, Manila, Philippines
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Kolluri N, Albarran N, Fan A, Olson A, Sagar M, Young A, Gomez-Marquez J, Klapperich CM. SNAPflex: a paper-and-plastic device for instrument-free RNA and DNA extraction from whole blood. LAB ON A CHIP 2020; 20:3386-3398. [PMID: 32766666 DOI: 10.1039/d0lc00277a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Nucleic acid amplification tests (NAATs), which amplify and detect pathogen nucleic acids, are vital methods to diagnose diseases, particularly in cases where patients exhibit low levels of infection. For many blood-borne pathogens such as HIV or Plasmodium falciparum, it is necessary to first extract pathogen RNA or DNA from patient blood prior to NAAT analysis. Traditional nucleic acid extraction methods are expensive, resource-intensive and are often difficult to deploy to resource-limited areas where many blood-borne infections are widespread. Here, we describe a portable, paper-and-plastic device, called SNAPflex, for instrument-free nucleic acid extraction from whole blood, which builds upon our previous work for RNA extraction using a pressure-driven extraction system. SNAPflex shows improved HIV RNA extraction from simulated patient samples compared to traditional extraction methods as well as long-term stability of extracted RNA without the need for cold storage. We further demonstrated successful extraction and recovery of P. falciparum DNA from cultured parasites in whole blood. SNAPflex was designed to be easily manufacturable and deployable to resource-limited settings.
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Affiliation(s)
- Nikunja Kolluri
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.
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50
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Thompson TA, Touré MB, Sanogo D, Shaffer JG, Doumbia SO, Krogstad DJ. Template copy number and the sensitivity of quantitative PCR for Plasmodium falciparum in asymptomatic individuals. Malar J 2020; 19:295. [PMID: 32811534 PMCID: PMC7436962 DOI: 10.1186/s12936-020-03365-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/10/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The identification of asymptomatic individuals with Plasmodium falciparum infection is difficult because they do not seek medical treatment and often have too few asexual parasites detectable using microscopy or rapid diagnostic tests (≤ 200 parasites per μl). Quantitative PCR (qPCR) may provide greater sensitivity and permits estimation of the initial template DNA concentration. This study examined the hypothesis that qPCR assays using templates with higher copy numbers may be more sensitive for P. falciparum than assays based on templates with lower copy numbers. METHODS To test this hypothesis, ten qPCR assays for DNA sequences with template copy numbers from 1 to 160 were compared using parasite DNA standards (n = 2) and smear-positive filter paper blots from asymptomatic smear-positive subjects (n = 96). RESULTS Based on the testing of P. falciparum parasite DNA standards and filter paper blots, cycle threshold values decreased as the concentrations of template DNA and template copy numbers increased (p < 0.001). Likewise, the analytical and clinical sensitivities of qPCR assays for P. falciparum DNA (based on DNA standards and filter paper blots, respectively) increased with template copy number. Despite the gains in clinical sensitivity from increased template copy numbers, qPCR assays failed to detect more than half of the filter paper blots with low parasite densities (≤ 200 asexual parasites per μl). CONCLUSIONS These results confirm the hypothesis that the sensitivity of qPCR for P. falciparum in the blood of individuals with asymptomatic infection increases with template copy number. However, because even the most sensitive qPCR assays (with template copy numbers from 32 to 160) detected fewer than 50% of infections with ≤ 200 asexual parasites per μl, the sensitivity of qPCR must be increased further to identify all smear-positive, asymptomatic individuals in order to interrupt transmission.
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Affiliation(s)
- Trevor A Thompson
- West African International Center of Excellence for Malaria Research, Bamako, Mali.
- Tulane School of Public Health and Tropical Medicine, 1430 Tulane Avenue, #8317, J.B. Johnston Building, Room 510, New Orleans, LA, 70112-2699, USA.
| | - Mahamoudou B Touré
- West African International Center of Excellence for Malaria Research, Bamako, Mali
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Daouda Sanogo
- West African International Center of Excellence for Malaria Research, Bamako, Mali
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jeffrey G Shaffer
- West African International Center of Excellence for Malaria Research, Bamako, Mali.
- Tulane School of Public Health and Tropical Medicine, 1430 Tulane Avenue, #8317, J.B. Johnston Building, Room 510, New Orleans, LA, 70112-2699, USA.
| | - Seydou O Doumbia
- West African International Center of Excellence for Malaria Research, Bamako, Mali
- University of the Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Donald J Krogstad
- West African International Center of Excellence for Malaria Research, Bamako, Mali.
- Tulane School of Public Health and Tropical Medicine, 1430 Tulane Avenue, #8317, J.B. Johnston Building, Room 510, New Orleans, LA, 70112-2699, USA.
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