1
|
Pian H, Wang H, Wang H, Li Z. Dual CRISPR/Cas13a Cascade Strand Displacement-Triggered Transcription for Point-of-Care Detection of Plasmodium in Asymptomatic Malaria. Anal Chem 2024; 96:7524-7531. [PMID: 38695755 DOI: 10.1021/acs.analchem.4c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
Asymptomatic infections of Plasmodium parasites are major obstacles to malaria control and elimination. A sensitive, specific, and user-friendly method is urgently needed for point-of-care (POC) Plasmodium diagnostics in asymptomatic malaria, especially in resource-limited settings. In this work, we present a POC method (termed Cas13a-SDT) based on the cascade sequence recognition and signal amplification of dual Cas13a trans-cleavage and strand displacement-triggered transcription (SDT). Cas13a-SDT not only achieves exceptional specificity in discriminating the target RNA from nontarget RNAs with any cross-interaction but also meets the sensitivity criterion set by the World Health Organization (WHO) for effective malaria detection. Remarkably, this novel method was successfully applied to screen malaria in asymptomatic infections from clinical samples. The proposed method provides a user-friendly and visually interpretable output mode while maintaining high accuracy and reliability comparable to RT-PCR. These excellent features demonstrate the significant potential of Cas13a-SDT for POC diagnosis of Plasmodium infections, laying a vital foundation for advancing malaria control and elimination efforts.
Collapse
Affiliation(s)
- Hongru Pian
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Honghong Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| |
Collapse
|
2
|
Nguyen TK, Jun H, Louis JM, Mazigo E, Lee WJ, Youm HC, Shin J, Lungu DK, Kanyemba C, Ahmed MA, Muh F, Lee SJ, Na S, Chun W, Park WS, No JH, Kim MJ, Han ET, Han JH. Enhancing malaria detection in resource-limited areas: A high-performance colorimetric LAMP assay for Plasmodium falciparum screening. PLoS One 2024; 19:e0298087. [PMID: 38335219 PMCID: PMC10857711 DOI: 10.1371/journal.pone.0298087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
Malaria eradication efforts in resource-limited areas require a rapid, economical, and accurate tool for detecting of the low parasitemia. The malaria rapid diagnostic test (mRDT) is the most suitable for on-site detection of the deadliest form of malaria, Plasmodium falciparum. However, the deletions of histidine rich protein 2 and 3 genes are known to compromise the effectiveness of mRDT. One of the approaches that have been explored intensively for on-site diagnostics is the loop-mediated isothermal amplification (LAMP). LAMP is a one-step amplification that allows the detection of Plasmodium species in less than an hour. Thus, this study aims to present a new primer set to enhance the performance of a colorimetric LAMP (cLAMP) for field application. The primer binding regions were selected within the A-type of P. falciparum 18S rRNA genes, which presents a dual gene locus in the genome. The test result of the newly designed primer indicates that the optimal reaction condition for cLAMP was 30 minutes incubation at 65°C, a shorter incubation time compared to previous LAMP detection methods that typically takes 45 to 60 minutes. The limit of detection (LoD) for the cLAMP using our designed primers and laboratory-grown P. falciparum (3D7) was estimated to be 0.21 parasites/μL which was 1,000-fold higher than referencing primers. Under optimal reaction condition, the new primer sets showed the sensitivity (100%, 95% CI: 80.49-100%) and specificity (100%, 95% CI: 94.64-100%) with 100% (95% CI: 95.70-100%) accuracy on the detection of dried blood spots from Malawi (n = 84). Briefly, the newly designed primer set for P. falciparum detection exhibited high sensitivity and specificity compared to referenced primers. One great advantage of this tool is its ability to be detected by the naked eye, enhancing field approaches. Thus, this tool has the potential to be effective for accurate early parasite detection in resource-limited endemic areas.
Collapse
Affiliation(s)
- Tuyet Kha Nguyen
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Hojong Jun
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Johnsy Mary Louis
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Ernest Mazigo
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Wang-Jong Lee
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | | | - Jieun Shin
- Noul Co., Ltd., Yongin, Gyeonggi-do, Republic of Korea
| | | | | | - Md Atique Ahmed
- ICMR-Regional Medical Research Centre, NER, Dibrugarh, Assam, India
| | - Fauzi Muh
- Faculty of Public Health, Department of Epidemiology and Tropical Diseases, Universitas Diponegoro, Semarang, Indonesia
| | - Se Jin Lee
- Department of Obstetrics and Gynecology, Kangwon National University Hospital, Chuncheon, Gangwon-do, Republic of Korea
| | - Sunghun Na
- Department of Obstetrics and Gynecology, Kangwon National University Hospital, Chuncheon, Gangwon-do, Republic of Korea
| | - Wanjoo Chun
- Department of Pharmacology, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Won Sun Park
- Department of Physiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Joo Hwan No
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Seongnam, Gyeonggi-do, Republic of Korea
| | - Min-Jae Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| |
Collapse
|
3
|
Xiu L, Li H, Hu Q, Zhang Y, Chen SB, Wang C, Zhou XN, Chen JH, Yin K. A versatile microfluidic platform for malaria infection screening and Plasmodium species genotyping. EBioMedicine 2023; 98:104898. [PMID: 38029461 PMCID: PMC10697993 DOI: 10.1016/j.ebiom.2023.104898] [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: 09/18/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Malaria, a widespread parasitic disease caused by Plasmodium species, remains a significant global health concern. Rapid and accurate detection, as well as species genotyping, are critical for effective malaria control. METHODS We have developed a Flexible, Robust, Equipment-free Microfluidic (FREM) platform, which integrates recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR)-based detection, enabling simultaneous malaria infection screening and Plasmodium species genotyping. The microfluidic chip enabled the parallel detection of multiple Plasmodium species, each amplified by universal RPA primers and genotyped by specific crRNAs. The inclusion of a sucrose solution effectively created spatial separation between the RPA and CRISPR assays within a one-pot system, effectively resolving compatibility issues. FINDINGS Clinical assessment of DNA extracts from patients with suspected malaria demonstrates the FREM platform's superior sensitivity (98.41%) and specificity (92.86%), yielding consistent results with PCR-sequencing for malaria detection, which achieved a positive predictive agreement of 98.41% and a negative predictive agreement of 92.86%. Additionally, the accuracy of species genotyping was validated through concordance rates of 90.91% between the FREM platform and PCR-sequencing. INTERPRETATION The FREM platform offers a promising solution for point-of-care malaria screening and Plasmodium species genotyping. It highlights the possibility of improving malaria control efforts and expanding its applicability to address other infectious diseases. FUNDING This work was financially supported by International Joint Laboratory on Tropical Diseases Control in Greater Mekong Subregion, National Natural Science Foundation of China, the Natural Science Foundation of Shanghai, Bill & Melinda Gates Foundation and National Research and Development Plan of China.
Collapse
Affiliation(s)
- Leshan Xiu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China.
| | - Huimin Li
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Qinqin Hu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Yuqian Zhang
- Department of Surgery, Division of Surgery Research, Mayo Clinic, Rochester, MN, 55905, USA; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
| | - Chenxi Wang
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China; Hainan Tropical Diseases Research Center (Hainan Sub-Center, Chinese Center for Tropical Diseases Research), Haikou, 571199, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China; Hainan Tropical Diseases Research Center (Hainan Sub-Center, Chinese Center for Tropical Diseases Research), Haikou, 571199, China.
| | - Kun Yin
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China.
| |
Collapse
|
4
|
Malaria Microscopy Competency in the Subnational Verification, China: Implications for Malaria Elimination and the Prevention of Malaria Reestablishment. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:8003845. [PMID: 36349187 PMCID: PMC9637463 DOI: 10.1155/2022/8003845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/15/2022] [Accepted: 10/19/2022] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Qualified microscopy competency is a key indicator for certification of malaria elimination. To better prepare the country certification and identify the priorities that need improvement to prevent malaria reestablishment, microscopy competency at different levels were assessed in subnational verification of malaria elimination in China. Methodology. Microscopist representatives from centers for disease control and prevention (CDC)/institutes of parasitic diseases (IPD) and medical institutes for malaria diagnosis at the provincial and county levels in the subnational verification were analyzed. Specifically, five provincial microscopist representatives and ten county-level representatives were assessed in each of previously endemic provinces on qualitative identification (Plasmodium positive or negative) and Plasmodium species identification using standard slides from the National Malaria Diagnosis Reference Laboratory. RESULTS A total of 100 provincial-level representatives (60 from 42 CDCs/IPDs and 40 from 34 medical institutes) and 200 county-level representatives (61 from 41 CDCs and 139 from 118 medical institutes) were included. The qualitative accuracy was higher than 90% each (P = 0.137), but slides with low parasite density were easy to be misdiagnosed as negative. Furthermore, the accuracy of species identification was 80.0% and 83.6% in medical institutes and centers for disease control and prevention (CDCs) at the provincial level (P = 0.407) with relatively high misdiagnosis of P. vivax as P. ovale in the latter (16.2%) and 82.0% and 85.0% in medical institutes and CDCs at the county level (P = 0.330) for the identification of P. falciparum and non-P. falciparum with higher false-negative in medical institutions (P < 0.001). CONCLUSIONS In conclusion, competent microscopy in subnational verification supported the quality in eliminating malaria in China, while the accurate identification of malaria parasites, especially slides with low parasite density still need to be improved through continuous diagnostic platform construction, continuous technological innovation, and targeted training to prevent reestablishment of malaria transmission.
Collapse
|
5
|
Zainabadi K, Lee MH, Walsh KF, Vilbrun SC, Mathurin LD, Ocheretina O, Pape JW, Fitzgerald DW. An optimized method for purifying, detecting and quantifying Mycobacterium tuberculosis RNA from sputum for monitoring treatment response in TB patients. Sci Rep 2022; 12:17382. [PMID: 36253384 PMCID: PMC9574834 DOI: 10.1038/s41598-022-19985-w] [Citation(s) in RCA: 1] [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: 05/27/2022] [Accepted: 09/07/2022] [Indexed: 02/05/2023] Open
Abstract
Diagnostics that more accurately detect and quantify viable Mycobacterium tuberculosis (Mtb) in the sputum of patients undergoing therapy are needed. Current culture- and molecular-based tests have shown limited efficacy for monitoring treatment response in TB patients, either due to the presence of viable sub-populations of Mtb which fail to grow under standard culture conditions (termed differentially detectable/culturable Mtb, DD Mtb) or the prolonged half-life of Mtb DNA in sputum. Here, we report an optimized RNA-based method for detecting and quantifying viable Mtb from patient sputum during the course of therapy. We first empirically derived a novel RNA extraction protocol from sputum that improves recovery of Mtb RNA while almost completely eliminating contamination from Mtb DNA and host nucleic acids. Next, we identified five Mtb 16S rRNA primer sets with varying limits of detection that were capable of distinguishing between live versus dead H37Rv Mtb. This combined protocol was then tested on sputa from a longitudinal cohort of patients receiving therapy for drug sensitive (DS) or drug resistant (DR) TB with first-line or second-line regimens, respectively. Results were compared with that of culture, including CFU, BACTEC MGIT, and a limiting dilution assay capable of detecting DD Mtb. The five 16S rRNA primer sets positively identified nearly all (range 94-100%) culture positive sputa, and a portion (19-37%) of culture negative sputa. In comparison, ten highly expressed Mtb mRNAs showed positivity in 72-86% of culture positive sputa, and in 0-13% of culture negative sputa. Two of the five 16S rRNA primer sets were able to positively identify 100% of culture positive sputa, and when tested on culture negative sputa from the DS cohort at 2 months post-initiation of therapy, identified 40% of samples as positive; a percentage that is in line with expected treatment failure rates when first-line therapy is discontinued early. These two primer sets also detected 16S rRNA in 13-20% of sputa at 6 months post-initiation of therapy in the DR cohort. Cycle threshold values for 16S rRNA showed a strong correlation with Mtb numbers as determined by culture (R > 0.87), including as Mtb numbers declined during the course of treatment with first-line and second-line regimens. The optimized molecular assay outlined here may have utility for monitoring treatment response in TB patients.
Collapse
Affiliation(s)
- Kayvan Zainabadi
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA.
| | - Myung Hee Lee
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA
| | - Kathleen Frances Walsh
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | - Jean William Pape
- Center for Global Health, Weill Cornell Medicine, New York, NY, USA
- Les Centres GHESKIO, Port-au-Prince, Haiti
| | | |
Collapse
|
6
|
Metagenomic Sequencing for the Diagnosis of Plasmodium spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients—A Proof-of-Principle Assessment. Int J Mol Sci 2022; 23:ijms231911150. [PMID: 36232449 PMCID: PMC9569645 DOI: 10.3390/ijms231911150] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Molecular diagnostic approaches are increasingly included in the diagnostic workup and even in the primary diagnosis of malaria in non-endemic settings, where it is difficult to maintain skillful microscopic malaria detection due to the rarity of the disease. Pathogen-specific nucleic acid amplification, however, bears the risk of overlooking other pathogens associated with febrile illness in returnees from the tropics. Here, we assessed the discriminatory potential of metagenomic sequencing for the identification of different Plasmodium species with various parasitemia in EDTA blood of malaria patients. Overall, the proportion of Plasmodium spp.-specific sequence reads in the assessed samples showed a robust positive correlation with parasitemia (Spearman r = 0.7307, p = 0.0001) and a robust negative correlation with cycle threshold (Ct) values of genus-specific real-time PCR (Spearman r = −0.8626, p ≤ 0.0001). Depending on the applied bioinformatic algorithm, discrimination on species level was successful in 50% (11/22) to 63.6% (14/22) instances. Limiting factors for the discrimination on species level were very low parasitemia, species-depending lacking availability of reliable reference genomes, and mixed infections with high variance of the proportion of the infecting species. In summary, metagenomic sequencing as performed in this study is suitable for the detection of malaria in human blood samples, but the diagnostic detection limit for a reliable discrimination on species level remains higher than for competing diagnostic approaches like microscopy and PCR.
Collapse
|
7
|
Han KT, Han ZY, Zainabadi K. Developing Molecular Surveillance Capacity for Asymptomatic and Drug-Resistant Malaria in a Resource-Limited Setting-Experiences and Lessons Learned. Am J Trop Med Hyg 2022; 107:222-230. [PMID: 35895423 PMCID: PMC9393433 DOI: 10.4269/ajtmh.21-0543] [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: 05/19/2021] [Accepted: 10/15/2021] [Indexed: 08/03/2023] Open
Abstract
The COVID-19 pandemic has highlighted the important role molecular surveillance plays in public health. Such capacity however is either weak or nonexistent in many low-income countries. This article outlines a 2-year effort to establish two high-throughput molecular surveillance laboratories in Myanmar for tracking asymptomatic and drug resistant Plasmodium falciparum malaria. The lessons learned from this endeavor may prove useful for others seeking to establish similar molecular surveillance capacity in other resource-limited settings.
Collapse
Affiliation(s)
- Kay Thwe Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Zay Yar Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Kayvan Zainabadi
- Center for Global Health, Weill Cornell Medicine, New York, New York
| |
Collapse
|
8
|
Nundu SS, Arima H, Simpson SV, Chitama BYA, Munyeku YB, Muyembe JJ, Mita T, Ahuka S, Culleton R, Yamamoto T. Low prevalence of Plasmodium falciparum parasites lacking pfhrp2/3 genes among asymptomatic and symptomatic school-age children in Kinshasa, Democratic Republic of Congo. Malar J 2022; 21:126. [PMID: 35439987 PMCID: PMC9020024 DOI: 10.1186/s12936-022-04153-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
Background Loss of efficacy of diagnostic tests may lead to untreated or mistreated malaria cases, compromising case management and control. There is an increasing reliance on rapid diagnostic tests (RDTs) for malaria diagnosis, with the most widely used of these targeting the Plasmodium falciparum histidine-rich protein 2 (PfHRP2). There are numerous reports of the deletion of this gene in P. falciparum parasites in some populations, rendering them undetectable by PfHRP2 RDTs. The aim of this study was to identify P. falciparum parasites lacking the P. falciparum histidine rich protein 2 and 3 genes (pfhrp2/3) isolated from asymptomatic and symptomatic school-age children in Kinshasa, Democratic Republic of Congo. Methods The performance of PfHRP2-based RDTs in comparison to microscopy and PCR was assessed using blood samples collected and spotted on Whatman 903™ filter papers between October and November 2019 from school-age children aged 6–14 years. PCR was then used to identify parasite isolates lacking pfhrp2/3 genes. Results Among asymptomatic malaria carriers (N = 266), 49%, 65%, and 70% were microscopy, PfHRP2_RDT, and pfldh-qPCR positive, respectively. The sensitivity and specificity of RDTs compared to PCR were 80% and 70% while the sensitivity and specificity of RDTs compared to microscopy were 92% and 60%, respectively. Among symptomatic malaria carriers (N = 196), 62%, 67%, and 87% were microscopy, PfHRP2-based RDT, pfldh-qPCR and positive, respectively. The sensitivity and specificity of RDTs compared to PCR were 75% and 88%, whereas the sensitivity and specificity of RDTs compared to microscopy were 93% and 77%, respectively. Of 173 samples with sufficient DNA for PCR amplification of pfhrp2/3, deletions of pfhrp2 and pfhrp3 were identified in 2% and 1%, respectively. Three (4%) of samples harboured deletions of the pfhrp2 gene in asymptomatic parasite carriers and one (1%) isolate lacked the pfhrp3 gene among symptomatic parasite carriers in the RDT positive subgroup. No parasites lacking the pfhrp2/3 genes were found in the RDT negative subgroup. Conclusion Plasmodium falciparum histidine-rich protein 2/3 gene deletions are uncommon in the surveyed population, and do not result in diagnostic failure. The use of rigorous PCR methods to identify pfhrp2/3 gene deletions is encouraged in order to minimize the overestimation of their prevalence. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04153-2.
Collapse
Affiliation(s)
- Sabin S Nundu
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan. .,Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan. .,Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo.
| | - Hiroaki Arima
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Shirley V Simpson
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Ben-Yeddy Abel Chitama
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Yannick Bazitama Munyeku
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Jean-Jacques Muyembe
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
| | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Steve Ahuka
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
| | - Richard Culleton
- Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan. .,Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Ehime, Japan.
| | - Taro Yamamoto
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| |
Collapse
|
9
|
Yimam Y, Mohebali M, Abbaszadeh Afshar MJ. Comparison of diagnostic performance between conventional and ultrasensitive rapid diagnostic tests for diagnosis of malaria: A systematic review and meta-analysis. PLoS One 2022; 17:e0263770. [PMID: 35143565 PMCID: PMC8830612 DOI: 10.1371/journal.pone.0263770] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 01/26/2022] [Indexed: 11/19/2022] Open
Abstract
Background Successful malaria treatment, control and elimination programs require accurate, affordable, and field-deployable diagnostic tests. A number of studies have directly compared diagnostic performance between the new ultrasensitive rapid diagnostic test (us-RDT) and conventional rapid diagnostic test (co-RDT) for detecting malaria. Thus, we undertook this review to directly compare pooled diagnostic performance of us-RDT and co-RDT for detection of malaria. Methods PubMed, Web of Science, Scopus, Embase, and ProQuest were searched from their inception until 31 January 2021 accompanied by forward and backward citations tracking. Two authors independently assessed the quality of included studies by RevMan5 software (using the QUADAS-2 checklist). Diagnostic accuracy estimates (sensitivity and specificity and others) were pooled using a random-effect model and 95% confidence interval (CI) in Stata 15 software. Results Fifteen studies with a total of 20,236 paired co-RDT and us-RDT tests were included in the meta-analysis. Molecular methods (15 studies) and immunoassay test (one study) were used as standard methods for comparison with co-RDT and us-RDT tests. The pooled sensitivity for co-RDT and us-RDT were 42% (95%CI: 25–62%) and 61% (95%CI: 47–73%), respectively, with specificity of 99% (95%CI: 98–100%) for co-RDT, and 99% (95%CI: 96–99%) for us-RDT. In asymptomatic individuals, the pooled sensitivity and specificity of co-RDT were 27% (95%CI: 8–58%) and 100% (95%CI: 97–100%), respectively, while us-RDT had a sensitivity of 50% (95%CI: 33–68%) and specificity of 98% (95%CI: 94–100%). In low transmission settings, pooled sensitivity for co-RDT was 36% (95%CI: 9 76%) and 62% (95%CI: 44 77%) for us RDT, while in high transmission areas, pooled sensitivity for co RDT and us RDT were 62% (95%CI: 39 80%) and 75% (95%CI: 57–87%), respectively. Conclusion The us-RDT test showed better performance than co-RDT test, and this characteristic is more evident in asymptomatic individuals and low transmission areas; nonetheless, additional studies integrating a range of climate, geography, and demographics are needed to reliably understand the potential of the us-RDT.
Collapse
Affiliation(s)
- Yonas Yimam
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Biology, Faculty of Natural and Computational Sciences, Woldia University, Woldia, Ethiopia
- * E-mail:
| | - Mehdi Mohebali
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Centers for Research of Endemic Parasites of Iran (CREPI), Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Abbaszadeh Afshar
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Department of Medical Parasitology and Mycology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| |
Collapse
|
10
|
Limited Reliability of the Molecular Detection of Plasmodium spp. from Incubated Blood Culture Samples for Forensic Purposes. Microorganisms 2022; 10:microorganisms10020406. [PMID: 35208861 PMCID: PMC8879611 DOI: 10.3390/microorganisms10020406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 12/10/2022] Open
Abstract
The suitability of incubated blood culture material for forensic molecular malaria diagnosis was assessed for non-endemic settings for cases in which the differential diagnosis malaria was initially overlooked. For the proof-of-principle assessment, residual blood culture materials from febrile patients from tropical Ghana were investigated by real-time PCR and compared with available historic microscopic results. In 2114 samples, for which microscopical results and real-time PCR results were available, microscopical results comprised 711 P. falciparum detections, 7 P. malariae detections, 1 microscopically not-further-discriminable Plasmodium spp. detection as well as 13 detections of mixed infections comprising 12 cases of P. falciparum/P. malariae co-infections and 1 case of a P. falciparum/P. ovale complex co-infection, while real-PCR indicated 558 P. falciparum detections, 95 P. malariae detections, 10 P. ovale complex detections, 1 P. vivax detection and 4 detected P. falciparum/P. malariae co-infections. Concordance of routine microscopy and real-time PCR was imperfect. Using routine microscopy as reference was associated with a seemingly low agreement of positive real-time PCR results of 90.9%. However, if positive samples, either by routine microscopy or real-time PCR or both, were applied as a combined reference, the agreement of positive results obtained with real-time PCR was increased from 74.0% to 77.9%, while the agreement of positive results obtained with routine microscopy was decreased from 100% to 85.3%. The predictive value of routine microscopy for negative results in the reference was slightly better with 90.9% compared to real-time PCR with 86.9%; the concordance between routine microscopy and real-time PCR was imperfect. In conclusion, even suboptimal sample materials such as incubated blood culture materials can be applied for forensic malaria diagnosis, if more suitable sample materials are not available, but the molecular detection rate of positive results in routine microscopy is much lower than previously reported for non-incubated blood.
Collapse
|
11
|
Performance and Application of Commercially Available Loop-Mediated Isothermal Amplification (LAMP) Kits in Malaria Endemic and Non-Endemic Settings. Diagnostics (Basel) 2021; 11:diagnostics11020336. [PMID: 33670618 PMCID: PMC7922894 DOI: 10.3390/diagnostics11020336] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 01/04/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a sensitive molecular tool suitable for use as a near point-of-care test for the diagnosis of malaria. Recent meta-analyses have detailed high sensitivity and specificity of malaria LAMP when compared to microscopy, rapid diagnostic tests, and polymerase chain reaction in both endemic and non-endemic settings. Despite this, the use of malaria LAMP has primarily been limited to research settings to date. In this review, we aim to assess to what extent commercially available malaria LAMP kits have been applied in different settings, and to identify possible obstacles that may have hindered their use from being adopted further. In order to address this, we conducted a literature search in PubMed.gov using the search terms (((LAMP) OR (Loop-mediated isothermal amplification)) AND ((Malaria) OR (Plasmodium))). Focusing primarily on studies employing one of the commercially available kits, we then selected three key areas of LAMP application for further review: the performance and application of LAMP in malaria endemic settings including low transmission areas; LAMP for malaria screening during pregnancy; and malaria LAMP in returning travelers in non-endemic settings.
Collapse
|