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Keita AK, Mbaye A, Soumah AK, Kadio KJJO, Diallo H, Gnimadi TAC, Koivogui JB, Povogui MK, Monemou JL, Traore B, Vidal N, Guichet E, Ayouba A, Delaporte E, Peeters M, Toure A, Keita AK. Use of strips of rapid diagnostic tests as a source of ribonucleic acid for genomic surveillance of viruses: an example of SARS-CoV-2. Virol J 2024; 21:171. [PMID: 39090721 PMCID: PMC11295317 DOI: 10.1186/s12985-024-02442-7] [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: 03/04/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND This study aimed to demonstrate that the genomic material of SARS-CoV-2 can be isolated from strips of COVID-19 rapid diagnostic test cassettes. METHOD It was a prospective cross-sectional study involving patients admitted to treatment centers and sampling sites in the city of Conakry, Guinea. A total of 121 patients were double sampled, and 9 more patients were tested only for RDT. PCR was conducted according to the protocol of the RunMei kit. Sequencing was performed by using the illumina COVIDSeq protocol. Nine COVID-19 RDTs without nasopharyngeal swabs were in addition tested. RESULT Among the 130 COVID-19 RDTs, forty-seven were macroscopically positive, whereas seventy-two were positive according to PCR using RDT strip, while among the 121 VTM swabs, sixty-four were positive. Among eighty-three negative COVID-19 RDTs, twenty-seven were positive by PCR using RDT strip with a geometric mean Ct value of 32.49 cycles. Compared to those of PCR using VTM, the sensitivity and specificity of PCR using RDT strip were estimated to be 100% and 85.96%, respectively, with 93.39% test accuracy. Among the fifteen COVID-19 RDT extracts eligible for sequencing, eleven had sequences identical to those obtained via the standard method, with coverage between 75 and 99.6%. CONCLUSION These results show that COVID-19 RDTs can be used as biological material for the genomic surveillance of SARS-CoV-2.
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Affiliation(s)
- Alpha Kabiné Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Aminata Mbaye
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea.
| | - Abdoul Karim Soumah
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Kadio Jean Jacques Olivier Kadio
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Haby Diallo
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Thibaut Armel Chérif Gnimadi
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Joel Balla Koivogui
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Moriba Kowa Povogui
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Jean Louis Monemou
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Baba Traore
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Nicole Vidal
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
| | - Emilande Guichet
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
| | - Ahidjo Ayouba
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
| | - Eric Delaporte
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
| | - Martine Peeters
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
| | - Abdoulaye Toure
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
| | - Alpha Kabinet Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université Gamal Abder Nasser de Conakry, Conakry, Guinea
- Institut de Recherche pour le Développement (IRD), INSERM, TransVIHMI, University of Montpellier, Montpellier, France
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El Hadji Ibrahima N, Diatta G, Adama Zan D, Bassene H, Sokhna C, Parola P. Quantitative Polymerase Chain Reaction from Malaria Rapid Diagnostic Tests to Detect Borrelia crocidurae, the Agent of Tick-Borne Relapsing Fever, in Febrile Patients in Senegal. Am J Trop Med Hyg 2023; 108:968-976. [PMID: 36913922 PMCID: PMC10160891 DOI: 10.4269/ajtmh.22-0342] [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: 05/20/2022] [Accepted: 10/29/2022] [Indexed: 03/14/2023] Open
Abstract
In endemic malaria areas, Plasmodium is currently diagnosed mainly through the use of rapid diagnostic tests (RDTs). However, in Senegal, many causes of fever remain unknown. Tick-borne relapsing fever, an often-neglected public health problem, is the main cause of consultation for acute febrile illness after malaria and flu in rural areas. Our objective was to test the feasibility of extracting and amplifying DNA fragments by quantitative polymerase chain reaction (qPCR) from malaria-negative RDTs for Plasmodium falciparum (malaria Neg RDTs P.f) to detect Borrelia spp. and other bacteria. Between January and December 2019, malaria Neg RDTs P.f were collected on a quarterly basis in 12 health facilities in four regions of Senegal. The DNA extracted from the malaria Neg RDTs P.f was tested using qPCR and the results were confirmed by standard PCR and sequencing. Only Borrelia crocidurae DNA was detected in 7.22% (159/2,202) of RDTs. The prevalence of B. crocidurae DNA was higher in July (16.47%, 43/261) and August (11.21%, 50/446). The annual prevalence was 9.2% (47/512) and 5.0% (12/241) in Ngayokhem and Nema-Nding, respectively, health facilities in the Fatick region. Our study confirms that B. crocidurae infection is a frequent cause of fever in Senegal, with a high prevalence of cases in health facilities in the regions of Fatick and Kaffrine. Malaria Neg RDTs P.f are potentially a good source of pathogen sampling for the molecular identification of other causes of fever of unknown origin, even in the most remote areas.
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Affiliation(s)
- Ndiaye El Hadji Ibrahima
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), APHM, SSA, Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France
- VITROME, IRD UMR 257, Campus International IRD-UCAD Hann, Dakar, Sénégal
| | - Georges Diatta
- VITROME, IRD UMR 257, Campus International IRD-UCAD Hann, Dakar, Sénégal
| | - Diarra Adama Zan
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), APHM, SSA, Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France
| | - Hubert Bassene
- VITROME, IRD UMR 257, Campus International IRD-UCAD Hann, Dakar, Sénégal
| | - Cheikh Sokhna
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France
- VITROME, IRD UMR 257, Campus International IRD-UCAD Hann, Dakar, Sénégal
| | - Philippe Parola
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), APHM, SSA, Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Marseille, France
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Singh K, Bharti PK, Devi NC, Ahmed N, Sharma A. Plasmodium malariae Detected by Microscopy in the International Bordering Area of Mizoram, a Northeastern State of India. Diagnostics (Basel) 2022; 12:diagnostics12082015. [PMID: 36010365 PMCID: PMC9407229 DOI: 10.3390/diagnostics12082015] [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: 06/22/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
Northeastern states of India share international borders with Myanmar, China, Bangladesh, and Bhutan, contributing 7.45% of the overall malaria cases in the country. Mizoram accounts for the highest malaria burden in the northeastern states, with perennial transmission in the hilly and deep-forested areas. Plasmodium falciparum (93%) is the most prevalent human Plasmodium species, followed by P. vivax; however, information on P. ovale and P. malariae is negligible. Rapid diagnostic tests (RDTs) are the most preferred malaria diagnostic tool followed by microscopy in this high malaria-endemic region. The present epidemiological study was carried out in July and August 2019 to assess the malaria burden in and around the Chawngte primary health center, Lawngtlai District of Mizoram, using RDTs and microscopy as diagnostic tools. World Health Organization-certified level I microscopists examined the blood smears. Diagnosis using RDTs resulted in 151 malaria cases (P. falciparum: 136; P. vivax: 15) out of 948 screened fever cases. However, blood smear examination detected 179 cases (P. falciparum: 154; P. vivax: 17; mixed P. falciparum + P. vivax infection: 3; P. malariae: 5). Analysis revealed that the risk of malaria infection was higher in the ≥5-year-old subjects than in the under-5 age group. The mean parasite density of P. malariae (1455.00/μL blood) was the lowest; cf. with P. falciparum: 12,275.08/μL blood. Surveillance at the point-of-care level using microscopy was able to detect all the four human Plasmodium species and their mixed infections, including P. malariae, which were missed with RDTs. Thus, the quality of microscopy along with trained manpower should be strengthened to diagnose all human malaria parasite species (particularly P. malariae and P. ovale) until the molecular tools are deployed at the field level to achieve malaria elimination by 2030.
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Affiliation(s)
- Kuldeep Singh
- ICMR—National Institute of Malaria Research, Field Station, Guwahati 781005, India
- Correspondence:
| | | | - Naorem Chaoba Devi
- ICMR—National Institute of Malaria Research, Field Station, Guwahati 781005, India
| | - Naseem Ahmed
- ICMR—National Institute of Malaria Research, New Delhi 110077, India
| | - Amit Sharma
- ICMR—National Institute of Malaria Research, New Delhi 110077, India
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
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4
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Andrianaranjaka VHI, Ravaoarisoa E, Rakotomanga TA, Ralinoro F, Rakoto DAD, Randrianarivo RH, Jeannoda V, Ratsimbasoa A. DNA recovery from used malaria RDT to detect Plasmodium species and to assess Plasmodium falciparum genetic diversity: a pilot study in Madagascar. Malar J 2022; 21:227. [PMID: 35883089 PMCID: PMC9327223 DOI: 10.1186/s12936-022-04246-y] [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: 01/12/2022] [Accepted: 07/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Rapid diagnostic tests (RDT) are widely used for malaria diagnosis in Madagascar, where Plasmodium falciparum is the predominant species. Molecular diagnosis is essential for malaria surveillance, but requires additional blood samples for DNA extraction. Used RDTs is an attractive alternative that can be used as a source of DNA. Plasmodium falciparum genetic diversity and multiplicity of infection, usually determined by the genotyping of polymorphic regions of merozoite surface proteins 1 and 2 genes (msp1, msp2), and the repeated region RII of the glutamate-rich protein gene (glurp) have been associated with malaria transmission levels and subsequently with the impact of the deployed control strategies. Thus, the study aims to use RDT as DNA source to detect Plasmodium species, to characterize Plasmodium falciparum genetic diversity and determine the multiplicity of infection. Methods A pilot study was conducted in two sites with different epidemiological patterns: Ankazomborona (low transmission area) and Matanga (high transmission area). On May 2018, used RDT (SD BIOLINE Malaria Ag P.f/Pan, 05FK63) were collected as DNA source. Plasmodium DNA was extracted by simple elution with nuclease free water. Nested-PCR were performed to confirm Plasmodium species and to analyse P. falciparum msp1, msp2 and glurp genes polymorphisms. Results Amongst the 170 obtained samples (N = 74 from Ankazomborona and N = 96 from Matanga), Plasmodium positivity rate was 23.5% (40/170) [95% CI 17.5–30.8%] by nested-PCR with 92.2% (37/40) positive to P. falciparum, 5% (2/40) to Plasmodium vivax and 2.5% (1/40) to P. falciparum/P. vivax mixed infection. Results showed high polymorphisms in P. falciparum msp1, msp2 and glurp genes. Multiple infection rate was 28.6% [95% CI 12.2–52.3%]. The mean of MOI was 1.79 ± 0.74. Conclusion This pilot study highlighted that malaria diagnosis and molecular analysis are possible by using used malaria RDT. A large-scale study needs to be conducted to assess more comprehensively malaria parasites transmission levels and provide new data for guiding the implementation of local strategies for malaria control and elimination. Trial registration Retrospectively registered
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Affiliation(s)
- Voahangy Hanitriniaina I Andrianaranjaka
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar. .,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar.
| | - Elisabeth Ravaoarisoa
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Tovonahary A Rakotomanga
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Fanomezantsoa Ralinoro
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Danielle A Doll Rakoto
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Ranjàna H Randrianarivo
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Victor Jeannoda
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Arsène Ratsimbasoa
- Faculté de Médecine, Université de Fianarantsoa, Fianarantsoa, Madagascar.,Centre National d'Application de Recherche Pharmaceutique, Antananarivo, Madagascar
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5
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Kagoro FM, Allen E, Mabuza A, Workman L, Magagula R, Kok G, Davies C, Malatje G, Guérin PJ, Dhorda M, Maude RJ, Raman J, Barnes KI. Making data map-worthy-enhancing routine malaria data to support surveillance and mapping of Plasmodium falciparum anti-malarial resistance in a pre-elimination sub-Saharan African setting: a molecular and spatiotemporal epidemiology study. Malar J 2022; 21:207. [PMID: 35768869 PMCID: PMC9244181 DOI: 10.1186/s12936-022-04224-4] [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: 02/02/2022] [Accepted: 05/29/2022] [Indexed: 11/15/2022] Open
Abstract
Background Independent emergence and spread of artemisinin-resistant Plasmodium falciparum malaria have recently been confirmed in Africa, with molecular markers associated with artemisinin resistance increasingly detected. Surveillance to promptly detect and effectively respond to anti-malarial resistance is generally suboptimal in Africa, especially in low transmission settings where therapeutic efficacy studies are often not feasible due to recruitment challenges. However, these communities may be at higher risk of anti-malarial resistance. Methods From March 2018 to February 2020, a sequential mixed-methods study was conducted to evaluate the feasibility of the near-real-time linkage of individual patient anti-malarial resistance profiles with their case notifications and treatment response reports, and map these to fine scales in Nkomazi sub-district, Mpumalanga, a pre-elimination area in South Africa. Results Plasmodium falciparum molecular marker resistance profiles were linked to 55.1% (2636/4787) of notified malaria cases, 85% (2240/2636) of which were mapped to healthcare facility, ward and locality levels. Over time, linkage of individual malaria case demographic and molecular data increased to 75.1%. No artemisinin resistant validated/associated Kelch-13 mutations were detected in the 2385 PCR positive samples. Almost all 2812 samples assessed for lumefantrine susceptibility carried the wildtype mdr86ASN and crt76LYS alleles, potentially associated with decreased lumefantrine susceptibility. Conclusion Routine near-real-time mapping of molecular markers associated with anti-malarial drug resistance on a fine spatial scale provides a rapid and efficient early warning system for emerging resistance. The lessons learnt here could inform scale-up to provincial, national and regional malaria elimination programmes, and may be relevant for other antimicrobial resistance surveillance. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04224-4.
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Affiliation(s)
- Frank M Kagoro
- Collaborating Centre for Optimising Antimalarial Therapy (CCOAT), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town (UCT), Cape Town, South Africa.,Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,WorldWide Antimalarial Resistance Network (WWARN), Southern African Regional Hub, Division of Clinical Pharmacology, Department of Medicine, UCT, Mbombela, South Africa.,Infectious Diseases Data Observatory (IDDO), Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth Allen
- Collaborating Centre for Optimising Antimalarial Therapy (CCOAT), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town (UCT), Cape Town, South Africa.,WorldWide Antimalarial Resistance Network (WWARN), Southern African Regional Hub, Division of Clinical Pharmacology, Department of Medicine, UCT, Mbombela, South Africa.,Infectious Diseases Data Observatory (IDDO), Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Aaron Mabuza
- Collaborating Centre for Optimising Antimalarial Therapy (CCOAT), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town (UCT), Cape Town, South Africa.,WorldWide Antimalarial Resistance Network (WWARN), Southern African Regional Hub, Division of Clinical Pharmacology, Department of Medicine, UCT, Mbombela, South Africa
| | - Lesley Workman
- Collaborating Centre for Optimising Antimalarial Therapy (CCOAT), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town (UCT), Cape Town, South Africa.,WorldWide Antimalarial Resistance Network (WWARN), Southern African Regional Hub, Division of Clinical Pharmacology, Department of Medicine, UCT, Mbombela, South Africa.,Infectious Diseases Data Observatory (IDDO), Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ray Magagula
- Mpumalanga Provincial Malaria Elimination Programme, Mbombela, Mpumalanga, South Africa
| | - Gerdalize Kok
- Mpumalanga Provincial Malaria Elimination Programme, Mbombela, Mpumalanga, South Africa
| | - Craig Davies
- Malaria Programme, Clinton Health Access Initiative, Pretoria, South Africa
| | - Gillian Malatje
- Mpumalanga Provincial Malaria Elimination Programme, Mbombela, Mpumalanga, South Africa
| | - Philippe J Guérin
- WorldWide Antimalarial Resistance Network (WWARN), Southern African Regional Hub, Division of Clinical Pharmacology, Department of Medicine, UCT, Mbombela, South Africa.,Infectious Diseases Data Observatory (IDDO), Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mehul Dhorda
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Infectious Diseases Data Observatory (IDDO), Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Richard J Maude
- Mahidol Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Harvard TH Chan School of Public Health, Harvard University, Boston, MA, USA.,The Open University, Milton Keynes, UK
| | - Jaishree Raman
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Disease, Johannesburg, Gauteng, South Africa.,Wits Research Institute for Malaria, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.,UP Institute for Sustainable Malaria Control, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Karen I Barnes
- Collaborating Centre for Optimising Antimalarial Therapy (CCOAT), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town (UCT), Cape Town, South Africa. .,WorldWide Antimalarial Resistance Network (WWARN), Southern African Regional Hub, Division of Clinical Pharmacology, Department of Medicine, UCT, Mbombela, South Africa. .,Infectious Diseases Data Observatory (IDDO), Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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6
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Hosch S, Yoboue CA, Donfack OT, Guirou EA, Dangy JP, Mpina M, Nyakurungu E, Blöchliger K, Guerra CA, Phiri WP, Ayekaba MO, García GA, Tanner M, Daubenberger C, Schindler T. Analysis of nucleic acids extracted from rapid diagnostic tests reveals a significant proportion of false positive test results associated with recent malaria treatment. Malar J 2022; 21:23. [PMID: 35073934 PMCID: PMC8785039 DOI: 10.1186/s12936-022-04043-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 01/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Surveillance programmes often use malaria rapid diagnostic tests (RDTs) to determine the proportion of the population carrying parasites in their peripheral blood to assess the malaria transmission intensity. Despite an increasing number of reports on false-negative and false-positive RDT results, there is a lack of systematic quality control activities for RDTs deployed in malaria surveillance programmes. METHODS The diagnostic performance of field-deployed RDTs used for malaria surveys was assessed by retrospective molecular analysis of the blood retained on the tests. RESULTS Of the 2865 RDTs that were collected in 2018 on Bioko Island and analysed in this study, 4.7% had a false-negative result. These false-negative RDTs were associated with low parasite density infections. In 16.6% of analysed samples, masked pfhrp2 and pfhrp3 gene deletions were identified, in which at least one Plasmodium falciparum strain carried a gene deletion. Among all positive RDTs analysed, 28.4% were tested negative by qPCR and therefore considered to be false-positive. Analysing the questionnaire data collected from the participants, this high proportion of false-positive RDTs could be explained by P. falciparum histidine rich protein 2 (PfHRP2) antigen persistence after recent malaria treatment. CONCLUSION Malaria surveillance depending solely on RDTs needs well-integrated quality control procedures to assess the extent and impact of reduced sensitivity and specificity of RDTs on malaria control programmes.
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Affiliation(s)
- Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Charlene Aya Yoboue
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | | | - Etienne A Guirou
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Jean-Pierre Dangy
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Maxmillian Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo, United Republic of Tanzania.,Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
| | - Elizabeth Nyakurungu
- Ifakara Health Institute, Bagamoyo, United Republic of Tanzania.,Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
| | - Koranan Blöchliger
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Carlos A Guerra
- Medical Care Development International, Malabo, Equatorial Guinea
| | - Wonder P Phiri
- Medical Care Development International, Malabo, Equatorial Guinea
| | | | | | - Marcel Tanner
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Claudia Daubenberger
- Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland. .,Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea.
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7
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Guirou EA, Schindler T, Hosch S, Donfack OT, Yoboue CA, Krähenbühl S, Deal A, Cosi G, Gondwe L, Mwangoka G, Masuki H, Salim N, Mpina M, Said J, Abdulla S, Hoffman SL, Nlavo BM, Maas C, Falla CC, Phiri WP, Garcia GA, Tanner M, Daubenberger C. Molecular malaria surveillance using a novel protocol for extraction and analysis of nucleic acids retained on used rapid diagnostic tests. Sci Rep 2020; 10:12305. [PMID: 32703999 PMCID: PMC7378824 DOI: 10.1038/s41598-020-69268-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/10/2020] [Indexed: 11/09/2022] Open
Abstract
The use of malaria rapid diagnostic tests (RDTs) as a source for nucleic acids that can be analyzed via nucleic acid amplification techniques has several advantages, including minimal amounts of blood, sample collection, simplified storage and shipping conditions at room temperature. We have systematically developed and extensively evaluated a procedure to extract total nucleic acids from used malaria RDTs. The co-extraction of DNA and RNA molecules from small volumes of dried blood retained on the RDTs allows detection and quantification of P. falciparum parasites from asymptomatic patients with parasite densities as low as 1 Pf/µL blood using reverse transcription quantitative PCR. Based on the extraction protocol we have developed the ENAR (Extraction of Nucleic Acids from RDTs) approach; a complete workflow for large-scale molecular malaria surveillance. Using RDTs collected during a malaria indicator survey we demonstrated that ENAR provides a powerful tool to analyze nucleic acids from thousands of RDTs in a standardized and high-throughput manner. We found several, known and new, non-synonymous single nucleotide polymorphisms in the propeller region of the kelch 13 gene among isolates circulating on Bioko Island, Equatorial Guinea.
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Affiliation(s)
- Etienne A Guirou
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Tobias Schindler
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Salome Hosch
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Charlene Aya Yoboue
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Silvan Krähenbühl
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Anna Deal
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Glenda Cosi
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Linda Gondwe
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo Branch, United Republic of Tanzania
| | - Grace Mwangoka
- Ifakara Health Institute, Bagamoyo Branch, United Republic of Tanzania
| | - Heavenlight Masuki
- Department of Paediatrics and Child Health, Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - Nahya Salim
- Department of Paediatrics and Child Health, Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - Maxmillian Mpina
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo Branch, United Republic of Tanzania
| | - Jongo Said
- Ifakara Health Institute, Bagamoyo Branch, United Republic of Tanzania
| | - Salim Abdulla
- Ifakara Health Institute, Bagamoyo Branch, United Republic of Tanzania
| | | | | | - Carl Maas
- Marathon EG Production Ltd, Malabo, Equatorial Guinea
| | | | - Wonder P Phiri
- Medical Care Development International, Malabo, Equatorial Guinea
| | | | - Marcel Tanner
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
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8
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Srisutham S, Suwannasin K, Mathema VB, Sriprawat K, Smithuis FM, Nosten F, White NJ, Dondorp AM, Imwong M. Utility of Plasmodium falciparum DNA from rapid diagnostic test kits for molecular analysis and whole genome amplification. Malar J 2020; 19:193. [PMID: 32460780 PMCID: PMC7251736 DOI: 10.1186/s12936-020-03259-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/15/2020] [Indexed: 11/10/2022] Open
Abstract
Background Rapid diagnostic tests (RDTs) have become the most common diagnostic tool for detection of Plasmodium falciparum malaria, in particular in remote areas. RDT blood spots provide a source of parasite DNA for molecular analysis. In this study, the utility of RDTs for molecular analysis and the performance of different methods for whole genome amplification were investigated. Methods Positive P. falciparum RDTs were collected from Kayin, Myanmar from August 2014 to January 2016. The RDT samples were stored for 6 months, 9 months, 20 months, 21 months, and 32 months before DNA extraction and subsequent molecular analysis of P. falciparum kelch 13 (pfkelch13) mutations, P. falciparum multidrug resistance 1 (pfmdr1), and P. falciparum plasmepsin 2 (pfplasmepsin2) gene amplification. In addition, performance of four whole genome amplification (WGA) kits were compared, including REPLI-g®, MALBACTM, PicoPLEX®, and GenomePlex®, for which DNA quantity and quality were compared between original DNA and post-WGA products. Results The proportion of successful amplification of the different molecular markers was similar between blood spots analysed from RDTs stored for 6, 9, 20, 21, or 32 months. Successful amplification was dependent on the molecular markers fragment length (p value < 0.05): 18% for a 1245 bp fragment of pfkelch13, 71% for 364 bp of pfkelch13, 81% for 87 bp of pfmdr1, 81% for 108 bp of pfplasmepsin2. Comparison of the four WGA assay kits showed that REPLI-g®, MALBACTM, and PicoPLEX® increased the quantity of DNA 60 to 750-fold, whereas the ratio of parasite DNA amplification over human DNA was most favourable for MALBAC®. Sequencing results of pfkelch13, P. falciparum chloroquine resistance transporter (pfcrt), P. falciparum dihydrofolate reductase (pfdhfr) and six microsatellite markers assessed from the post-WGA product was the same as from the original DNA. Conclusions Blood spots from RDTs are a good source for molecular analysis of P. falciparum, even after storage up to 32 months. WGA of RDT-derived parasite DNA reliably increase DNA quantity with sufficient quality for molecular analysis of resistance markers.
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Affiliation(s)
- Suttipat Srisutham
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kanokon Suwannasin
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Vivek Bhakta Mathema
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Frank M Smithuis
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Medical Action Myanmar, Yangon, Myanmar
| | - Francois Nosten
- Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas J White
- 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, UK
| | - 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, 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. .,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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9
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Guiguemde KT, Dieye Y, Lô AC, Ndiaye M, Lam A, Manga IA, Sow GD, Diop M, Souané T, Diouf MP, Tine RCK, Faye B. Molecular detection and quantification of Plasmodium falciparum gametocytes carriage in used RDTs in malaria elimination settings in northern Senegal. Malar J 2020; 19:123. [PMID: 32228599 PMCID: PMC7106854 DOI: 10.1186/s12936-020-03204-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/23/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Malaria surveillance requires powerful tools and strategies to achieve malaria elimination. Rapid diagnostic tests for malaria (RDTs) are easily deployed on a large scale and are helpful sources of parasite DNA. The application of sensitive molecular techniques to these RDTs is a modern tool for improving malaria case detection and drug resistance surveillance. Several studies have made it possible to extract the DNA of Plasmodium falciparum from RDTs. The knowledge of gametocyte carriage in the population is important to better assess the level of parasite transmission in elimination settings. The aim of this study was to detect P. falciparum gametocytes from used RDTs by quantitative PCR for molecular monitoring of malaria transmission. METHODS DNA was extracted from 303 RDT devices (SD Bioline Malaria Pf) using the Chelex-100 protocol. qPCR was performed in a 20 μL reaction to detect and quantify transcripts of the pfs25 gene. The cycle threshold (Ct) was determined by the emission fluorescence corresponding to the initial amount of amplified DNA. RESULTS The study found an overall prevalence of 53.47% with an average Ct of 32.12 ± 4.28 cycles. In 2018, the prevalence of gametocytes was higher in the Ranérou district (76.24%) than in the Saint-Louis district (67.33%) where an increase in the number of gametocyte carriers in 2018 was noted, in comparison with 2017. CONCLUSIONS RDTs are a good source of DNA for molecular monitoring of gametocyte carriage. This method is a simple and effective tool to better understand the level of malaria transmission with a view to elimination.
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Affiliation(s)
| | - Yakou Dieye
- PATH, Malaria Control and Evaluation Partnership (MACEPA), Dakar, Senegal
| | - Aminata Collé Lô
- Department of Medical Parasitology, Medical Faculty, Cheikh Anta Diop University, Dakar, Senegal
| | - Magatte Ndiaye
- Department of Medical Parasitology, Medical Faculty, Cheikh Anta Diop University, Dakar, Senegal
| | - Aminata Lam
- Department of Medical Parasitology, Medical Faculty, Cheikh Anta Diop University, Dakar, Senegal
| | - Isaac Akhénaton Manga
- Department of Medical Parasitology, Medical Faculty, Cheikh Anta Diop University, Dakar, Senegal
| | - Gnagna Dieng Sow
- PATH, Malaria Control and Evaluation Partnership (MACEPA), Dakar, Senegal
| | - Moussa Diop
- PATH, Malaria Control and Evaluation Partnership (MACEPA), Dakar, Senegal
| | - Tamba Souané
- PATH, Malaria Control and Evaluation Partnership (MACEPA), Dakar, Senegal
| | - Marie Pièrre Diouf
- Department of Medical Parasitology, Medical Faculty, Cheikh Anta Diop University, Dakar, Senegal
| | - Roger Clément Kouly Tine
- Department of Medical Parasitology, Medical Faculty, Cheikh Anta Diop University, Dakar, Senegal
| | - Babacar Faye
- Department of Medical Parasitology, Medical Faculty, Cheikh Anta Diop University, Dakar, Senegal
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10
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DNA recovery from archived RDTs for genetic characterization of Plasmodium falciparum in a routine setting in Lambaréné, Gabon. Malar J 2019; 18:336. [PMID: 31578142 PMCID: PMC6775649 DOI: 10.1186/s12936-019-2972-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/24/2019] [Indexed: 11/15/2022] Open
Abstract
Background Rapid diagnostic tests (RDTs) have been described as a source of genetic material to analyse malaria parasites in proof-of-concept studies. The increasing use of RDTs (e.g., in focal or mass screening and treatment campaigns) makes this approach particularly attractive for large-scale investigations of parasite populations. In this study, the complexity of Plasmodium falciparum infections, parasite load and chloroquine resistance transporter gene mutations were investigated in DNA samples extracted from positive RDTs, obtained in a routine setting and archived at ambient temperature. Methods A total of 669 archived RDTs collected from malaria cases in urban, semi-urban and rural areas of central Gabon were used for P. falciparum DNA extraction. Performance of RDTs as a source of DNA for PCR was determined using: (i) amplification of a single copy merozoite surface protein 1 (msp1) gene followed by highly sensitive and automated capillary electrophoresis; (ii) genotyping of the pfcrt gene locus 72–76 using haplotype-specific-probe-based real-time PCR to characterize chloroquine resistance; and, (iii) real-time PCR targeting 18S genes to detect and quantify Plasmodium parasites. Results Out of the 669 archived RDTs, amplification of P. falciparum nucleic materials had a success rate of 97% for 18S real-time PCR, and 88% for the msp1 gene. The multiplicity of infections (MOI) of the whole population was 2.6 (95% CI 2.5–2.8). The highest number of alleles detected in one infection was 11. The MOI decreased with increasing age (β = − 0.0046, p = 0.02) and residence in Lambaréné was associated with smaller MOIs (p < 0.001). The overall prevalence of mutations associated with chloroquine resistance was 78.5% and was not associated with age. In Lambaréné, prevalence of chloroquine resistance was lower compared to rural Moyen-Ogooué (β = − 0.809, p-value = 0.011). Conclusion RDT is a reliable source of DNA for P. falciparum detection and genotyping assays. Furthermore, the increasing use of RDTs allows them to be an alternative source of DNA for large-scale genetic epidemiological studies. Parasite populations in the study area are highly diverse and prevalence of chloroquine-resistant P. falciparum remains high, especially in rural areas.
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11
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Ishengoma DS, Saidi Q, Sibley CH, Roper C, Alifrangis M. Deployment and utilization of next-generation sequencing of Plasmodium falciparum to guide anti-malarial drug policy decisions in sub-Saharan Africa: opportunities and challenges. Malar J 2019; 18:267. [PMID: 31477109 PMCID: PMC6719357 DOI: 10.1186/s12936-019-2853-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/22/2019] [Indexed: 01/13/2023] Open
Abstract
Parasite resistance against anti-malarial drugs is a major threat to the ongoing malaria control and elimination strategies. This is especially true since resistance to the currently recommended artemisinins and partner drugs has been confirmed in South East Asia (SEA) and new anti-malarial compounds are not expected to be available in the near future. Spread from SEA or independent emergence of artemisinin resistance in sub-Saharan Africa (SSA) could reverse the achievements in malaria control that have been attained in the past two decades and derail the ongoing elimination strategies. The current surveillance of clinical efficacy and resistance to anti-malarial drugs is based on efficacy trials to assess the clinical performance of anti-malarials, in vivo/ex vivo assessment of parasite susceptibility to anti-malarials and prevalence of known molecular markers of drug resistance. Whereas clinical efficacy trials are restricted by cost and the complex logistics of patient follow-up, molecular detection of genetic mutations associated with resistance or reduced susceptibility to anti-malarials is by contrast a simple and powerful tool for early detection and monitoring of the prevalence of resistant parasites at population level. This provides needed information before clinical failure emerges, allowing policy makers to anticipate problems and respond. The various methods previously used in detection of molecular markers of drug resistance share some limitations: low-throughput, and high costs per sample and demanding infrastructure. However, recent technological advances including next-generation sequencing (NGS) methodologies promise greatly increased throughput and reduced costs, essentially providing unprecedented potential to address different research and operational questions of relevance for drug policy. This review assesses the potential role of NGS to provide comprehensive information that could guide drug policies in malaria endemic countries and looks at the foreseeable challenges facing the establishment of NGS approaches for routine surveillance of parasite resistance to anti-malarials in SSA.
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Affiliation(s)
- Deus S Ishengoma
- National Institute for Medical Research, Tanga Centre, Tanga, Tanzania.
| | - Queen Saidi
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Carol H Sibley
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Cally Roper
- London School of Hygiene & Tropical Medicine, London, UK
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
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12
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Raman J, Kagoro FM, Mabuza A, Malatje G, Reid A, Frean J, Barnes KI. Absence of kelch13 artemisinin resistance markers but strong selection for lumefantrine-tolerance molecular markers following 18 years of artemisinin-based combination therapy use in Mpumalanga Province, South Africa (2001-2018). Malar J 2019; 18:280. [PMID: 31438951 PMCID: PMC6704579 DOI: 10.1186/s12936-019-2911-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/13/2019] [Indexed: 11/28/2022] Open
Abstract
Background The ability of Plasmodium falciparum parasites to develop resistance to widely used anti-malarials threatens malaria control and elimination efforts. Regular drug efficacy monitoring is essential for ensuring effective treatment policies. In low transmission settings where therapeutic efficacy studies are often not feasible, routine surveillance for molecular markers associated with anti-malarial resistance provides an alternative for the early detection of emerging resistance. Such a longitudinal survey of changes in the prevalence of selected molecular markers of resistance was conducted in the malaria-endemic regions of Mpumalanga Province, South Africa, where malaria elimination at a district-level is being pursued. Methods Molecular analyses to determine the prevalence of alleles associated with resistance to lumefantrine (mdr86N, crt76K and mdr1 copy number variation) and sulfadoxine–pyrimethamine (dhfr triple, dhps double, SP quintuple) were conducted between 2001 and 2018, while artemisinin resistance markers (kelch13 mutations) were assessed only in 2018. Results Parasite DNA was successfully amplified from 1667/2393 (70%) of malaria-positive rapid diagnostic tests routinely collected at primary health care facilities. No artemisinin resistance-associated kelch13 mutations nor amplification of the mdr1 gene copy number associated with lumefantrine resistance were observed. However, prevalence of both the mdr86N and crt76K alleles increased markedly over the study period, with all isolates collected in 2018 carrying these markers. SP quintuple mutation prevalence increased steadily from 14% in 2001 to 96% in 2018. Mixed alleles at any of the codons assessed were rare by 2018. Conclusion No kelch13 mutations confirmed or suspected to be associated with artemisinin resistance were identified in 2018. Although parasites carrying the mdr86N and crt76K alleles associated with reduced lumefantrine susceptibility were strongly selected for over the study period, nearing fixation by 2018, the marker for lumefantrine resistance, namely increased mdr1 copy number, was not observed in this study. The increase in mdr86N and crt76K allele prevalence together with intense regional artemether–lumefantrine drug pressure, raises concern regarding the sustained artemether–lumefantrine efficacy. Regular, rigorous anti-malarial resistance marker surveillance across all three South African malaria-endemic provinces to inform case management is recommended.
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Affiliation(s)
- Jaishree Raman
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Sandringham, Johannesburg, Gauteng, South Africa. .,Wits Research Institute for Malaria, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa. .,UP Institute for Sustainable Malaria Control, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
| | - Frank M Kagoro
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa.,Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Aaron Mabuza
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Gillian Malatje
- Mpumalanga Provincial Malaria Elimination Programme, Nelspruit, Mpumalanga, South Africa
| | - Anthony Reid
- Operational Research Unit, Médecins Sans Frontières, Operational Centre, Brussels, Luxembourg
| | - John Frean
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Sandringham, Johannesburg, Gauteng, South Africa.,Wits Research Institute for Malaria, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Karen I Barnes
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
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13
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Proof of concept: used malaria rapid diagnostic tests applied for parallel sequencing for surveillance of molecular markers of anti-malarial resistance in Bissau, Guinea-Bissau during 2014-2017. Malar J 2019; 18:252. [PMID: 31349834 PMCID: PMC6660714 DOI: 10.1186/s12936-019-2894-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/23/2019] [Indexed: 01/17/2023] Open
Abstract
Background Large-scale surveillance of molecular markers of anti-malarial drug resistance is an attractive method of resistance monitoring, to complement therapeutic efficacy studies in settings where the latter are logistically challenging. Methods Between 2014 and 2017, this study sampled malaria rapid diagnostic tests (RDTs), used in routine clinical care, from two health centres in Bissau, Guinea-Bissau. In order to obtain epidemiological insights, RDTs were collected together with patient data on age and sex. A subset of positive RDTs from one of the two sites (n = 2184) were tested for Plasmodium DNA content. Those testing positive for Plasmodium DNA by PCR (n = 1390) were used for library preparation, custom designed dual indexing and next generation Miseq targeted sequencing of Plasmodium falciparum genes pfcrt, pfmdr1, pfdhfr, pfdhps and pfk13. Results The study found a high frequency of the pfmdr1 codon 86N at 88–97%, a significant decrease of the pfcrt wildtype CVMNK haplotype and elevated levels of the pfdhfr/pfdhps quadruple mutant ranging from 33 to 51% between 2014 and 2017. No polymorphisms indicating artemisinin tolerance were discovered. The demographic data indicate a large proportion of young adults (66%, interquartile range 11–28 years) presenting with P. falciparum infections. While a total of 5532 gene fragments were successfully analysed on a single Illumina Miseq flow cell, PCR-positivity from the library preparation varied considerably from 13 to 87% for different amplicons. Furthermore, pre-screening of samples for Plasmodium DNA content proved necessary prior to library preparation. Conclusions This study serves as a proof of concept for using leftover clinical material (used RDTs) for large-scale molecular surveillance, encompassing the inherent complications regarding to methodology and analysis when doing so. Factors such as RDT storage prior to DNA extraction and parasitaemia of the infection are likely to have an effect on whether or not parasite DNA can be successfully analysed, and are considered part of the reason the data yield is suboptimal. However, given the necessity of molecular surveillance of anti-malarial resistance in settings where poor infrastructure, poor economy, lack of educated staff and even surges of political instability remain major obstacles to performing clinical studies, obtaining the necessary data from used RDTs, despite suboptimal output, becomes a feasible, affordable and hence a justifiable method. Electronic supplementary material The online version of this article (10.1186/s12936-019-2894-8) contains supplementary material, which is available to authorized users.
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14
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Molecular quantification of Plasmodium parasite density from the blood retained in used RDTs. Sci Rep 2019; 9:5107. [PMID: 30911048 PMCID: PMC6434039 DOI: 10.1038/s41598-019-41438-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/05/2019] [Indexed: 12/27/2022] Open
Abstract
Most malaria-endemic countries are heavily reliant upon rapid diagnostic tests (RDT) for malaria case identification and treatment. RDT previously used for malaria diagnosis can subsequently be used for molecular assays, including qualitative assessment of parasite species present or the carriage of resistance markers, because parasite DNA can be extracted from the blood inside the RDT which remains preserved on the internal components. However, the quantification of parasite density has not previously been possible from used RDT. In this study, blood samples were collected from school-age children in Western Kenya, in the form of both dried blood spots on Whatman filter paper, and the blood spot that is dropped into rapid diagnostic tests during use. Having first validated a robotic DNA extraction method, the parasite density was determined from both types of sample by duplex qPCR, and across a range of densities. The methods showed good agreement. The preservation of both parasite and human DNA on the nitrocellulose membrane inside the RDT was stable even after more than one year's storage. This presents a useful opportunity for researchers or clinicians wishing to gain greater information about the parasite populations that are being studied, without significant investment of resources.
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15
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Loop-mediated isothermal amplification (LAMP) and Polymerase Chain Reaction (PCR) as quality assurance tools for Rapid Diagnostic Test (RDT) malaria diagnosis in Northern Namibia. PLoS One 2018; 13:e0206848. [PMID: 30540744 PMCID: PMC6291133 DOI: 10.1371/journal.pone.0206848] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/19/2018] [Indexed: 11/19/2022] Open
Abstract
Malaria cases sometimes go undetected using RDTs due to their inaccurate use, poor storage conditions and failure to detect low parasitaemia (<50parasites/μL). This could result in continuous transmission of malaria and sustenance of parasite reservoirs. Molecular diagnostic tools are more sensitive and specific than RDTs in the detection of plasmodium parasites. However, the Polymerase Chain Reaction (PCR) is not routinely used because equipment and reagents are expensive and requires highly skilled personnel. Loop-mediated isothermal amplification (LAMP) is a relatively new molecular diagnostic tool for malaria with all the advantages of PCR (sensitive and specific) without the mentioned disadvantages. However, it has not been evaluated extensively as a point of care diagnostic in the field. One hundred and fifteen used RDTs were collected from health facilities in Northern Namibia in a blind study and PCR and LAMP were used to determine the presence of Plasmodium DNA. The sensitivities and PPV were 40.91% and 90% respectively for RDTs, 72.73% and 100% respectively for PCR with LAMP as the golden standard. In low malaria transmission settings, LAMP can be also be considered for use as a surveillance tool to detect all sources of malaria and determine proportion of low parasitaemia infections in order to eliminate them.
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16
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Kitutu FE, Wamani H, Selling KE, Katabazi FA, Kuteesa RB, Peterson S, Kalyango JN, Mårtensson A. Can malaria rapid diagnostic tests by drug sellers under field conditions classify children 5 years old or less with or without Plasmodium falciparum malaria? Comparison with nested PCR analysis. Malar J 2018; 17:365. [PMID: 30326926 PMCID: PMC6192306 DOI: 10.1186/s12936-018-2508-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/06/2018] [Indexed: 01/02/2023] Open
Abstract
Background Malaria rapid diagnostic tests (RDTs) available as dipsticks or strips, are simple to perform, easily interpretable and do not require electricity nor infrastructural investment. Correct interpretation of and compliance with the RDT results is a challenge to drug sellers. Thus, drug seller interpretation of RDT strips was compared with laboratory scientist re-reading, and PCR analysis of Plasmodium DNA extracted from RDT nitrocellulose strips and fast transient analysis (FTA) cards. Malaria RDT cassettes were also assessed as a potential source of Plasmodium DNA. Methods A total of 212 children aged between 2 and 60 months, 199 of whom had complete records at two study drug shops in south western Uganda participated in the study. Duplicate 5 μL samples of capillary blood were picked from the 212 children, dispensed onto the sample well of the CareStart™ Pf-HRP2 RDT cassette and a FTA, Whatman™ 3MM filter paper in parallel. The RDT strip was interpreted by the drug seller within 15–20 min, visually re-read centrally by laboratory scientist and from it; Plasmodium DNA was recovered and detected by PCR, and compared with FTA recovered P. falciparum DNA PCR detection. Results Malaria positive samples were 62/199 (31.2%, 95% CI 24.9, 38.3) by drug seller interpretation of RDT strip, 59/212 (27.8%, 95% CI 22.2, 34.3) by laboratory scientist, 55/212 (25.9%, 95% CI 20.0, 32.6) by RDT nitrocellulose strip PCR and 64/212 (30.2%, 95% CI 24.4, 37.7). The overall agreement between the drug seller interpretation and laboratory scientist re-reading of the RDT strip was 93.0% with kappa value of 0.84 (95% CI 0.75, 0.92). The drug seller compliance with the reported RDT results was 92.5%. The performance of the three diagnostic strategies compared with FTA-PCR as the gold standard had sensitivity between 76.6 and 86.9%, specificity above 90%, positive predictive values ranging from 79.0 to 89.8% and negative predictive values above 90%. Conclusion Drug sellers can use RDTs in field conditions and achieve acceptable accuracy for malaria diagnosis, and they comply with the RDT results. Plasmodium DNA can be recovered from RDT nitrocellulose strips even in the context of drug shops. Future malaria surveillance and diagnostic quality control studies with RDT cassette as a source of Plasmodium DNA are recommended. Electronic supplementary material The online version of this article (10.1186/s12936-018-2508-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Freddy Eric Kitutu
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden. .,Pharmacy Department, Makerere University College of Health Sciences, Kampala, Uganda.
| | - Henry Wamani
- School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Katarina Ekholm Selling
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
| | - Fred Ashaba Katabazi
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Ronald Bisaso Kuteesa
- Infectious Disease Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Stefan Peterson
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden.,School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda.,UNICEF, Health Section, 3 UN Plaza, New York, NY, 10017, USA
| | - Joan Nakayaga Kalyango
- Pharmacy Department, Makerere University College of Health Sciences, Kampala, Uganda.,Clinical Epidemiology and Biostatistics Unit, Makerere University College of Health Sciences, Kampala, Uganda
| | - Andreas Mårtensson
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
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17
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Boyce RM, Hathaway N, Fulton T, Reyes R, Matte M, Ntaro M, Mulogo E, Waltmann A, Bailey JA, Siedner MJ, Juliano JJ. Reuse of malaria rapid diagnostic tests for amplicon deep sequencing to estimate Plasmodium falciparum transmission intensity in western Uganda. Sci Rep 2018; 8:10159. [PMID: 29977002 PMCID: PMC6033881 DOI: 10.1038/s41598-018-28534-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/25/2018] [Indexed: 01/29/2023] Open
Abstract
Molecular techniques are not routinely employed for malaria surveillance, while cross-sectional, community-based parasite surveys require significant resources. Here, we describe a novel use of malaria rapid diagnostic tests (RDTs) collected at a single facility as source material for sequencing to esimtate malaria transmission intensity across a relatively large catchment area. We extracted Plasmodium falciparum DNA from RDTs, then amplified and sequenced a region of the apical membrane antigen 1 (pfama1) using targeted amplicon deep sequencing. We determined the multiplicity of infection (MOI) for each sample and examined associations with demographic, clinical, and spatial factors. We successfully genotyped 223 of 287 (77.7%) of the samples. We demonstrated an inverse relationship between the MOI and elevation with individuals presenting from the highest elevation villages harboring infections approximately half as complex as those from the lowest (MOI 1.85 vs. 3.51, AOR 0.25, 95% CI 0.09-0.65, p = 0.004). This study demonstrates the feasibility and validity of using routinely-collected RDTs for molecular surveillance of malaria and has real-world utility, especially as the cost of high-throughpout sequencing continues to decline.
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Affiliation(s)
- Ross M Boyce
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA.
| | - Nick Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, 368 Plantation St., Worcester, Massachusetts, 01605, USA
| | - Travis Fulton
- Division of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health, 135 Dauer Drive, Chapel Hill, 27599, USA
| | - Raquel Reyes
- Division of General Medicine & Clinical Epidemiology, University of North Carolina at Chapel Hill, 5039 Old Clinic Building, CB 7110, Chapel Hill, 27599, USA
| | - Michael Matte
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Moses Ntaro
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Edgar Mulogo
- Department of Community Health, Mbarara University of Science & Technology, P.O. Box 1410, Mbarara, Uganda
| | - Andreea Waltmann
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA
| | - Jeffrey A Bailey
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, 368 Plantation St., Worcester, Massachusetts, 01605, USA
| | - Mark J Siedner
- Department of Medicine, Harvard Medical School and Massachusetts General Hospital, 125 Nashua Street, Suite 722, Boston, 02114, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, 130 Mason Farm Road, Chapel Hill, 27599, USA.,Division of Epidemiology, University of North Carolina at Chapel Hill Gillings School of Global Public Health, 135 Dauer Drive, Chapel Hill, 27599, USA.,Curriculum in Genetics and Microbiology, University of North Carolina at Chapel Hill, 321 South Columbia Street, Chapel Hill, NC, 27516, USA
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18
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Ndiaye M, Sow D, Nag S, Sylla K, Tine RC, Ndiaye JL, Lo AC, Gaye O, Faye B, Alifrangis M. Country-Wide Surveillance of Molecular Markers of Antimalarial Drug Resistance in Senegal by Use of Positive Malaria Rapid Diagnostic Tests. Am J Trop Med Hyg 2017; 97:1593-1596. [PMID: 29140232 PMCID: PMC5817740 DOI: 10.4269/ajtmh.17-0021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/16/2017] [Indexed: 11/22/2022] Open
Abstract
In Senegal, antimalarial drugs used in treatment and prevention of malaria are one of the main reasons for the current success in controlling malaria. However, the successful control of malaria is highly dependent on continued effectiveness of these drugs which may be compromised by the spread of drug resistance. Therefore, surveillance of drug resistance in the malaria parasites is essential. The objective of this pilot study was to test the feasibility of routinely sampled malaria rapid diagnostic tests (RDTs) at a national scale to assess the temporal changes in the molecular profiles of antimalarial drug resistance markers of Plasmodium falciparum parasites. Overall, 9,549 positive malaria RDTs were collected from 14 health facilities across the country. A limited random set of RDTs were analyzed regarding Pfcrt gene polymorphisms at codon 72-76. Overall, a high but varied prevalence (> 50%) of the wild-type CVMNK haplotype was observed including a higher CVMNK prevalence in the northern part (75%) compared with the southern part of the country (59%). With caution, the study provides a proof of concept that reuse of discarded P. falciparum positive RDTs can be applied in large-scale surveillance of antimalarial drug resistance.
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Affiliation(s)
- Magatte Ndiaye
- Service de Parasitologie–Mycologie, Faculté de Médecine, Université Cheikh Anta DIOP, Dakar, Sénégal
| | - Doudou Sow
- Service de Parasitologie–Mycologie, Faculté de Médecine, Université Cheikh Anta DIOP, Dakar, Sénégal
| | - Sidsel Nag
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Disease, Copenhagen University Hospital, Copenhagen, Denmark
| | - Khadime Sylla
- Service de Parasitologie–Mycologie, Faculté de Médecine, Université Cheikh Anta DIOP, Dakar, Sénégal
| | - Roger Clement Tine
- Service de Parasitologie–Mycologie, Faculté de Médecine, Université Cheikh Anta DIOP, Dakar, Sénégal
| | - Jean Louis Ndiaye
- Service de Parasitologie–Mycologie, Faculté de Médecine, Université Cheikh Anta DIOP, Dakar, Sénégal
| | - Aminata Collé Lo
- Service de Parasitologie–Mycologie, Faculté de Médecine, Université Cheikh Anta DIOP, Dakar, Sénégal
| | - Oumar Gaye
- Service de Parasitologie–Mycologie, Faculté de Médecine, Université Cheikh Anta DIOP, Dakar, Sénégal
| | - Babacar Faye
- Service de Parasitologie–Mycologie, Faculté de Médecine, Université Cheikh Anta DIOP, Dakar, Sénégal
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Disease, Copenhagen University Hospital, Copenhagen, Denmark
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19
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Donald W, Pasay C, Guintran JO, Iata H, Anderson K, Nausien J, Gresty KJ, Waters NC, Vestergaard LS, Taleo G, Cheng Q. The Utility of Malaria Rapid Diagnostic Tests as a Tool in Enhanced Surveillance for Malaria Elimination in Vanuatu. PLoS One 2016; 11:e0167136. [PMID: 27902755 PMCID: PMC5130254 DOI: 10.1371/journal.pone.0167136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/09/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND As part of efforts to eliminate malaria, Vanuatu has piloted the implementation of enhanced malaria surveillance and response strategies since 2011. This involves passive case detection (PCD) in health facilities, proactive case detection (Pro-ACD) and reactive case detection (Re-ACD) in communities using malaria rapid diagnostic tests (RDTs). While RDTs improve case management, their utility for detection of malaria infections in ACDs in this setting is unclear. METHODS The utility of malaria RDTs as diagnostic tools was evaluated in PCD, in five rounds of Pro-ACDs and five rounds of Re-ACDs conducted in Tafea and Torba Provinces between 2011 and 2014. The number of malaria infections detected by RDTs was compared to that detected by PCR from collected used-RDTs. RESULTS PCD in Tafea Province (2013) showed a RDT-positive rate of 0.21% (2/939) and a PCR-positive rate of 0.44% (2/453), indicating less than 1% of suspected malaria cases in Tafea Province were due to malaria. In Pro-ACDs conducted in Tafea and Torba Provinces, RDT-positive rates in 2013 and 2014 were 0.14% (3/2145) and 0% (0/2823), respectively, while the corresponding PCR-positive rates were 0.72% (9/1242) and 0.79% (9/1141). PCR identified villages in both provinces appearing to be transmission foci with a small number of low-density infections, mainly P. falciparum infections. In five rounds of Re-ACD, RDTs did not identify any additional infections while PCR detected only one among 173 subjects screened. CONCLUSIONS PCD and Pro-ACDs demonstrate that both Tafea and Torba Provinces in Vanuatu has achieved very low malaria prevalence. In these low-transmission areas, conducting Pro-ACD and Re-ACDs using RDTs appears not cost-effective and may have limited impact on interrupting malaria transmission due to the small number of infections identified by RDTs and considerable operational resources invested. More sensitive, field deployable and affordable diagnostic tools will improve malaria surveillance in malaria elimination settings.
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Affiliation(s)
- Wesley Donald
- Malaria & Vector Borne Diseases Control (MVBDC), Ministry of Health, Port Vila Vanuatu
| | - Cielo Pasay
- Drug Resistance and Diagnostics, Australian Army Malaria Institute, Brisbane, Australia
- Clinical Tropical Medicine, QIMR-Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Harry Iata
- Malaria & Vector Borne Diseases Control (MVBDC), Ministry of Health, Port Vila Vanuatu
| | - Karen Anderson
- Drug Resistance and Diagnostics, Australian Army Malaria Institute, Brisbane, Australia
- Clinical Tropical Medicine, QIMR-Berghofer Medical Research Institute, Brisbane, Australia
| | - Johnny Nausien
- Malaria & Vector Borne Diseases Control (MVBDC), Ministry of Health, Port Vila Vanuatu
| | - Karryn J Gresty
- Drug Resistance and Diagnostics, Australian Army Malaria Institute, Brisbane, Australia
- Clinical Tropical Medicine, QIMR-Berghofer Medical Research Institute, Brisbane, Australia
| | - Norman C. Waters
- Walter Reed Army Institute of Research, Malaria Vaccine Branch, Military Malaria Research Program, Silver Spring, Maryland, United States of America
| | | | - George Taleo
- Malaria & Vector Borne Diseases Control (MVBDC), Ministry of Health, Port Vila Vanuatu
- * E-mail: (QC); (GT)
| | - Qin Cheng
- Drug Resistance and Diagnostics, Australian Army Malaria Institute, Brisbane, Australia
- Clinical Tropical Medicine, QIMR-Berghofer Medical Research Institute, Brisbane, Australia
- * E-mail: (QC); (GT)
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20
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Mushi AK, Massaga JJ, Mandara CI, Mubyazi GM, Francis F, Kamugisha M, Urassa J, Lemnge M, Mgohamwende F, Mkude S, Schellenberg JA. Acceptability of malaria rapid diagnostic tests administered by village health workers in Pangani District, North eastern Tanzania. Malar J 2016; 15:439. [PMID: 27567531 PMCID: PMC5002154 DOI: 10.1186/s12936-016-1495-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 08/16/2016] [Indexed: 11/10/2022] Open
Abstract
Background Malaria continues to top the list of the ten most threatening diseases to child survival in Tanzania. The country has a functional policy for appropriate case management of malaria with rapid diagnostic tests (RDTs) from hospital level all the way to dispensaries, which are the first points of healthcare services in the national referral system. However, access to these health services in Tanzania is limited, especially in rural areas. Formalization of trained village health workers (VHWs) can strengthen and extend the scope of public health services, including diagnosis and management of uncomplicated malaria in resource-constrained settings. Despite long experience with VHWs in various health interventions, Tanzania has not yet formalized its involvement in malaria case management. This study presents evidence on acceptability of RDTs used by VHWs in rural northeastern Tanzania. Methods A cross-sectional study using quantitative and qualitative approaches was conducted between March and May 2012 in Pangani district, northeastern Tanzania, on community perceptions, practices and acceptance of RDTs used by VHWs. Results Among 346 caregivers of children under 5 years old, no evidence was found of differences in awareness of HIV rapid diagnostic tests and RDTs (54 vs. 46 %, p = 0.134). Of all respondents, 92 % expressed trust in RDT results, 96 % reported readiness to accept RDTs by VHWs, while 92 % expressed willingness to contribute towards the cost of RDTs used by VHWs. Qualitative results matched positive perceptions, attitudes and acceptance of mothers towards the use of RDTs by VHWs reported in the household surveys. Appropriate training, reliable supplies, affordability and close supervision emerged as important recommendations for implementation of RDTs by VHWs. Conclusion RDTs implemented by VHWs are acceptable to rural communities in northeastern Tanzania. While families are willing to contribute towards costs of sustaining these services, policy decisions for scaling-up will need to consider the available and innovative lessons for successful universally accessible and acceptable services in keeping with national health policy and sustainable development goals.
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Affiliation(s)
- Adiel K Mushi
- Centre for Enhancement of Effective Malaria Interventions, 2448, Barack Obama Drive, P.O. Box 9653, Dar es Salaam, Tanzania. .,National Institute for Medical Research, HQ, 3 Barack Obama Drive, 11101, Dar es Salaam, Tanzania.
| | - Julius J Massaga
- Centre for Enhancement of Effective Malaria Interventions, 2448, Barack Obama Drive, P.O. Box 9653, Dar es Salaam, Tanzania.,National Institute for Medical Research, HQ, 3 Barack Obama Drive, 11101, Dar es Salaam, Tanzania
| | - Celine I Mandara
- National Institute for Medical Research, Tanga Centre, P.O. Box 5004, Tanga, Tanzania
| | - Godfrey M Mubyazi
- Centre for Enhancement of Effective Malaria Interventions, 2448, Barack Obama Drive, P.O. Box 9653, Dar es Salaam, Tanzania.,National Institute for Medical Research, HQ, 3 Barack Obama Drive, 11101, Dar es Salaam, Tanzania
| | - Filbert Francis
- National Institute for Medical Research, Tanga Centre, P.O. Box 5004, Tanga, Tanzania
| | - Mathias Kamugisha
- National Institute for Medical Research, Tanga Centre, P.O. Box 5004, Tanga, Tanzania
| | - Jenesta Urassa
- National Institute for Medical Research, HQ, 3 Barack Obama Drive, 11101, Dar es Salaam, Tanzania
| | - Martha Lemnge
- National Institute for Medical Research, Tanga Centre, P.O. Box 5004, Tanga, Tanzania
| | - Fidelis Mgohamwende
- National malaria Control Programme, Ministry of Health and Social Welfare, 6 Samora Machel Avenue, 11478, Dar es Salaam, Tanzania
| | - Sigbert Mkude
- National malaria Control Programme, Ministry of Health and Social Welfare, 6 Samora Machel Avenue, 11478, Dar es Salaam, Tanzania
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21
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Msellemu D, Namango HI, Mwakalinga VM, Ntamatungiro AJ, Mlacha Y, Mtema ZJ, Kiware S, Lobo NF, Majambere S, Dongus S, Drakeley CJ, Govella NJ, Chaki PP, Killeen GF. The epidemiology of residual Plasmodium falciparum malaria transmission and infection burden in an African city with high coverage of multiple vector control measures. Malar J 2016; 15:288. [PMID: 27216734 PMCID: PMC4877954 DOI: 10.1186/s12936-016-1340-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/11/2016] [Indexed: 12/11/2022] Open
Abstract
Background In the Tanzanian city of Dar es Salaam, high coverage of long-lasting insecticidal nets (LLINs), larvicide application (LA) and mosquito-proofed housing, was complemented with improved access to artemisinin-based combination therapy and rapid diagnostic tests by the end of 2012. Methods Three rounds of city-wide, cluster-sampled cross-sectional surveys of malaria parasite infection status, spanning 2010 to 2012, were complemented by two series of high-resolution, longitudinal surveys of vector density. Results Larvicide application using a granule formulation of Bacillus thuringiensis var. israelensis (Bti) had no effect upon either vector density (P = 0.820) or infection prevalence (P = 0.325) when managed by a private-sector contractor. Infection prevalence rebounded back to 13.8 % in 2010, compared with <2 % at the end of a previous Bti LA evaluation in 2008. Following transition to management by the Ministry of Health and Social Welfare (MoHSW), LA consistently reduced vector densities, first using the same Bti granule in early 2011 [odds ratio (OR) (95 % confidence interval (CI)) = 0.31 (0.14, 0.71), P = 0.0053] and then a pre-diluted aqueous suspension formulation from mid 2011 onwards [OR (95 % CI) = 0.15 (0.07, 0.30), P ≪ 0.000001]. While LA by MoHSW with the granule formulation was associated with reduced infection prevalence [OR (95 % CI) = 0.26 (0.12, 0.56), P = 0.00040], subsequent liquid suspension use, following a mass distribution to achieve universal coverage of LLINs that reduced vector density [OR (95 % CI) = 0.72 (0.51, 1.01), P = 0.057] and prevalence [OR (95 % CI) = 0.80 (0.69, 0.91), P = 0.0013], was not associated with further prevalence reduction (P = 0.836). Sleeping inside houses with complete window screens only reduced infection risk [OR (95 % CI) = 0.71 (0.62, 0.82), P = 0.0000036] if the evenings and mornings were also spent indoors. Furthermore, infection risk was only associated with local vector density [OR (95 % CI) = 6.99 (1.12, 43.7) at one vector mosquito per trap per night, P = 0.037] among the minority (14 %) of households lacking screening. Despite attenuation of malaria transmission and immunity, 88 % of infected residents experienced no recent fever, only 0.4 % of these afebrile cases had been treated for malaria, and prevalence remained high (9.9 %) at the end of the study. Conclusions While existing vector control interventions have dramatically attenuated malaria transmission in Dar es Salaam, further scale-up and additional measures to protect against mosquito bites outdoors are desirable. Accelerated elimination of chronic human infections persisting at high prevalence will require active, population-wide campaigns with curative drugs. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1340-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Msellemu
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania.,Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
| | - Hagai I Namango
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania.,School of Biological Sciences, University of Nairobi, Nairobi, Kenya
| | - Victoria M Mwakalinga
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Alex J Ntamatungiro
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania.,Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
| | - Yeromin Mlacha
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Zacharia J Mtema
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | - Samson Kiware
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania.,Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, USA
| | - Neil F Lobo
- Eck Institute for Global Health, Notre Dame University, Notre Dame, IN, USA
| | - Silas Majambere
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Stefan Dongus
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Christopher J Drakeley
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
| | - Nicodem J Govella
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Prosper P Chaki
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania.,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Gerry F Killeen
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania. .,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
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22
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Vongsouvath M, Phommasone K, Sengvilaipaseuth O, Kosoltanapiwat N, Chantratita N, Blacksell SD, Lee SJ, de Lamballerie X, Mayxay M, Keomany S, Newton PN, Dubot-Pérès A. Using Rapid Diagnostic Tests as a Source of Viral RNA for Dengue Serotyping by RT-PCR - A Novel Epidemiological Tool. PLoS Negl Trop Dis 2016; 10:e0004704. [PMID: 27159058 PMCID: PMC4861341 DOI: 10.1371/journal.pntd.0004704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/20/2016] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Dengue virus infection causes major public health problems in tropical and subtropical areas. In many endemic areas, including the Lao PDR, inadequate access to laboratory facilities is a major obstacle to surveillance and study of dengue epidemiology. Filter paper is widely used for blood collection for subsequent laboratory testing for antibody and nucleic acid detection. For the first time, we demonstrate that dengue viral RNA can be extracted from dengue rapid diagnostic tests (RDT) and then submitted to real-time RT-PCR for serotyping. METHODOLOGY/PRINCIPAL FINDINGS We evaluated the Standard Diagnostics (SD) Bioline Dengue Duo RDT, a commonly used test in dengue endemic areas. First, using the QIAamp RNA kit, dengue RNA was purified from the sample pad of the NS1 RDT loaded with virus isolates of the four serotypes, then quantified by RT-PCR. We observed greater recovery of virus, with a mean of 27 times more RNA recovered from RDT, than from filter paper. Second, we evaluated dengue NS1 RDTs from patients at Mahosot Hospital, Vientiane, (99 patients) and from rural Salavan Provincial Hospital (362 patients). There was good agreement between dengue RT-PCR from NS1 RDT with RT-PCR performed on RNA extracted from patient sera, either using RDT loaded with blood (82.8% and 91.4%, in Vientiane and Salavan, respectively) or serum (91.9% and 93.9%). There was 100% concordance between RDT and serum RT-PCR of infecting dengue serotype. CONCLUSIONS/SIGNIFICANCE Therefore, the collection of NS1 positive RDTs, which do not require cold storage, may be a novel approach for dengue serotyping by RT-PCR and offers promising prospects for the collection of epidemiological data from previously inaccessible tropical areas to aid surveillance and public health interventions.
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Affiliation(s)
- Manivanh Vongsouvath
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Koukeo Phommasone
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Onanong Sengvilaipaseuth
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
- Mahidol - Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
| | - Stuart D. Blacksell
- Mahidol - Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Sue J. Lee
- Mahidol - Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Salaya, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Xavier de Lamballerie
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP) & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
- Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
| | - Sommay Keomany
- Salavan Provincial Hospital, Salavan Provincial Health Department, Salavan Province, Laos
| | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
| | - Audrey Dubot-Pérès
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford, United Kingdom
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP) & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
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23
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Nabet C, Doumbo S, Jeddi F, Sagara I, Manciulli T, Tapily A, L'Ollivier C, Djimde A, Doumbo OK, Piarroux R. Analyzing Deoxyribose Nucleic Acid from Malaria Rapid Diagnostic Tests to Study Plasmodium falciparum Genetic Diversity in Mali. Am J Trop Med Hyg 2016; 94:1259-65. [PMID: 27001760 DOI: 10.4269/ajtmh.15-0832] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/15/2016] [Indexed: 11/07/2022] Open
Abstract
We evaluated the use of positive malaria rapid diagnostic tests (mRDTs) to determine genetic diversity of Plasmodium falciparum in Mali. Genetic diversity was assessed via multiple loci variable number of tandem repeats analysis (MLVA). We performed DNA extraction from 104 positive and 30 negative used mRDTs that had been stored at ambient temperature for up to 14 months. Extracted DNA was analyzed via quantitative polymerase chain reaction (qPCR), and MLVA genotyping was then assessed on positive qPCR samples. Eighty-three of the positive mRDTs (83/104, 79.8%) and none of the negative mRDTs were confirmed P. falciparum positive via qPCR. We achieved complete genotyping of 90.4% (75/83) of the qPCR-positive samples. Genotyping revealed high genetic diversity among P. falciparum populations in Mali and an absence of population clustering. We show that mRDTs are useful to monitor P. falciparum genetic diversity and thereby can provide essential data to guide malaria control programs.
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Affiliation(s)
- Cécile Nabet
- UMR MD3 Infections Parasitaires Transmission Pharmacologie et Thérapeutique (IP-TPT), Aix-Marseille University, Marseilles, France; Parasitology Laboratory, Timone Hospital, Marseilles, France; Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, UMI 3189, Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technology, Bamako, Mali; University of Pavia, Pavia, Italy
| | - Safiatou Doumbo
- UMR MD3 Infections Parasitaires Transmission Pharmacologie et Thérapeutique (IP-TPT), Aix-Marseille University, Marseilles, France; Parasitology Laboratory, Timone Hospital, Marseilles, France; Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, UMI 3189, Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technology, Bamako, Mali; University of Pavia, Pavia, Italy
| | - Fakhri Jeddi
- UMR MD3 Infections Parasitaires Transmission Pharmacologie et Thérapeutique (IP-TPT), Aix-Marseille University, Marseilles, France; Parasitology Laboratory, Timone Hospital, Marseilles, France; Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, UMI 3189, Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technology, Bamako, Mali; University of Pavia, Pavia, Italy
| | - Issaka Sagara
- UMR MD3 Infections Parasitaires Transmission Pharmacologie et Thérapeutique (IP-TPT), Aix-Marseille University, Marseilles, France; Parasitology Laboratory, Timone Hospital, Marseilles, France; Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, UMI 3189, Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technology, Bamako, Mali; University of Pavia, Pavia, Italy
| | - Tommaso Manciulli
- UMR MD3 Infections Parasitaires Transmission Pharmacologie et Thérapeutique (IP-TPT), Aix-Marseille University, Marseilles, France; Parasitology Laboratory, Timone Hospital, Marseilles, France; Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, UMI 3189, Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technology, Bamako, Mali; University of Pavia, Pavia, Italy
| | - Amadou Tapily
- UMR MD3 Infections Parasitaires Transmission Pharmacologie et Thérapeutique (IP-TPT), Aix-Marseille University, Marseilles, France; Parasitology Laboratory, Timone Hospital, Marseilles, France; Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, UMI 3189, Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technology, Bamako, Mali; University of Pavia, Pavia, Italy
| | - Coralie L'Ollivier
- UMR MD3 Infections Parasitaires Transmission Pharmacologie et Thérapeutique (IP-TPT), Aix-Marseille University, Marseilles, France; Parasitology Laboratory, Timone Hospital, Marseilles, France; Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, UMI 3189, Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technology, Bamako, Mali; University of Pavia, Pavia, Italy
| | - Abdoulaye Djimde
- UMR MD3 Infections Parasitaires Transmission Pharmacologie et Thérapeutique (IP-TPT), Aix-Marseille University, Marseilles, France; Parasitology Laboratory, Timone Hospital, Marseilles, France; Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, UMI 3189, Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technology, Bamako, Mali; University of Pavia, Pavia, Italy
| | - Ogobara K Doumbo
- UMR MD3 Infections Parasitaires Transmission Pharmacologie et Thérapeutique (IP-TPT), Aix-Marseille University, Marseilles, France; Parasitology Laboratory, Timone Hospital, Marseilles, France; Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, UMI 3189, Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technology, Bamako, Mali; University of Pavia, Pavia, Italy
| | - Renaud Piarroux
- UMR MD3 Infections Parasitaires Transmission Pharmacologie et Thérapeutique (IP-TPT), Aix-Marseille University, Marseilles, France; Parasitology Laboratory, Timone Hospital, Marseilles, France; Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, UMI 3189, Faculty of Medicine and Dentistry, University of Sciences, Techniques and Technology, Bamako, Mali; University of Pavia, Pavia, Italy
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24
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Rapid Point-of-Care Diagnosis of Malaria and Dengue Infection. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Papa Mze N, Ndiaye YD, Diedhiou CK, Rahamatou S, Dieye B, Daniels RF, Hamilton EJ, Diallo M, Bei AK, Wirth DF, Mboup S, Volkman SK, Ahouidi AD, Ndiaye D. RDTs as a source of DNA to study Plasmodium falciparum drug resistance in isolates from Senegal and the Comoros Islands. Malar J 2015; 14:373. [PMID: 26415927 PMCID: PMC4587814 DOI: 10.1186/s12936-015-0861-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/23/2015] [Indexed: 11/29/2022] Open
Abstract
Background The World Health Organization has recommended rapid diagnostic tests (RDTs) for use in the diagnosis of suspected malaria cases. In addition to providing quick and accurate detection of Plasmodium parasite proteins in the blood, these tests can be used as sources of DNA for further genetic studies. As sulfadoxine-pyrimethamine is used currently for intermittent presumptive treatment of pregnant women in both Senegal and in the Comoros Islands, resistance mutations in the dhfr and dhps genes were investigated using DNA extracted from RDTs. Methods The proximal portion of the nitrocellulose membrane of discarded RDTs was used for DNA extraction. This genomic DNA was amplified using HRM to genotype the molecular markers involved in resistance to sulfadoxine-pyrimethamine: dhfr (51, 59, 108, and 164) and dhps (436, 437, 540, 581, and 613). Additionally, the msp1 and msp2 genes were amplified to determine the average clonality between Grande-Comore (Comoros) and Thiès (Senegal). Results A total of 201 samples were successfully genotyped at all codons by HRM; whereas, in 200 msp1 and msp2 genes were successfully amplified and genotyped by nested PCR. A high prevalence of resistance mutations were observed in the dhfr gene at codons 51, 59, and 108 as well as in the dhps gene at codons 437 and 436. A novel mutant in dhps at codon positions 436Y/437A was observed. The dhfr I164L codon and dhps K540 and dhps A581G codons had 100 % wild type alleles in all samples. Conclusion The utility of field-collected RDTs was validated as a source of DNA for genetic studies interrogating frequencies of drug resistance mutations, using two different molecular methods (PCR and High Resolution Melting). RDTs should not be discarded after use as they can be a valuable source of DNA for genetic and epidemiological studies in sites where filter paper or venous blood collected samples are nonexistent. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0861-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nasserdine Papa Mze
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal.
| | - Yaye Die Ndiaye
- Laboratoire of Parasitology and Mycology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, 5005, Dakar, Senegal.
| | - Cyrille K Diedhiou
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal.
| | - Silai Rahamatou
- Laboratory of National Malaria Control Programme, Moroni, Comoros.
| | - Baba Dieye
- Laboratoire of Parasitology and Mycology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, 5005, Dakar, Senegal.
| | - Rachel F Daniels
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA.
| | - Elizabeth J Hamilton
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Mouhamadou Diallo
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal.
| | - Amy K Bei
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal. .,Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA.
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA. .,Broad Institute: The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Souleymane Mboup
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal.
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, 02115, USA. .,Broad Institute: The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,School of Nursing and Health Sciences, Simmons College, Boston, MA, 02115, USA.
| | - Ambroise D Ahouidi
- Laboratory of Bacteriology-Virology, Hospital Aristide Le Dantec, 7325, Dakar, Senegal.
| | - Daouda Ndiaye
- Laboratoire of Parasitology and Mycology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, 5005, Dakar, Senegal.
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Morris U, Xu W, Msellem MI, Schwartz A, Abass A, Shakely D, Cook J, Bhattarai A, Petzold M, Greenhouse B, Ali AS, Björkman A, Fröberg G, Mårtensson A. Characterising temporal trends in asymptomatic Plasmodium infections and transporter polymorphisms during transition from high to low transmission in Zanzibar, 2005-2013. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 33:110-7. [PMID: 25917493 PMCID: PMC10445533 DOI: 10.1016/j.meegid.2015.04.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/14/2015] [Accepted: 04/18/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Improved understanding of the asymptomatic malaria parasite reservoir is a prerequisite to pursue malaria elimination efforts. We therefore characterised temporal trends and transporter polymorphisms in asymptomatic Plasmodium infections during the transition from high to low transmission in Zanzibar. METHODS Healthy individuals participating in cross-sectional surveys conducted 2005-2013 were screened for asymptomatic malaria by PCR. Complexity/diversity of infection and transporter polymorphisms were assessed in Plasmodium falciparum positive samples. Symptomatic samples were included for comparison of polymorphisms in 2013. RESULTS PCR-determined parasite prevalence declined from 21.1% (CI95% 17.4-24.9) to 2.3% (CI95% 1.7-2.9) from 2005 to 2013. P. falciparum remained the predominant species; prevalence was highest in children and young adults aged 5-25 years. Parasite densities and complexity of infection, but not population genetic diversity of P. falciparum, decreased from 2005-2009. pfcrt 76T (99.2-64.7%, p < 0.001) and pfmdr1 86Y frequencies (89.4-66.7%, p = 0.03) decreased over time. Pfmdr1 (a.a.86,184,1246) YYY and YYD haplotypes were more frequent in asymptomatic than symptomatic infections in 2013 (p < 0.001). CONCLUSIONS There is a declining, albeit persistent, reservoir of parasites present at low-densities in asymptomatic individuals in Zanzibar. This study revealed important characteristics of the remaining parasite population, including intriguing temporal trends in molecular markers associated with antimalarial resistance, which need to be further investigated.
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Affiliation(s)
- Ulrika Morris
- Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Weiping Xu
- Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Mwinyi I Msellem
- Zanzibar Malaria Elimination Programme (ZAMEP), Ministry of Health, Zanzibar, Tanzania
| | - Alanna Schwartz
- Department of Medicine, University of California San Francisco, CA, USA
| | - Ali Abass
- Zanzibar Malaria Elimination Programme (ZAMEP), Ministry of Health, Zanzibar, Tanzania
| | - Delér Shakely
- Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Medicine, Kungälv Hospital, Kungälv, Sweden
| | - Jackie Cook
- Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Zanzibar Malaria Elimination Programme (ZAMEP), Ministry of Health, Zanzibar, Tanzania
| | - Achuyt Bhattarai
- Malaria Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Max Petzold
- Health Metrics at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, CA, USA
| | - Abdullah S Ali
- Zanzibar Malaria Elimination Programme (ZAMEP), Ministry of Health, Zanzibar, Tanzania
| | - Anders Björkman
- Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gabrielle Fröberg
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Mårtensson
- Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden; Centre for Clinical Research Sörmland, Uppsala University, Sweden
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27
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Masanja IM, McMorrow ML, Maganga MB, Sumari D, Udhayakumar V, McElroy PD, Kachur SP, Lucchi NW. Quality assurance of malaria rapid diagnostic tests used for routine patient care in rural Tanzania: microscopy versus real-time polymerase chain reaction. Malar J 2015; 14:85. [PMID: 25889613 PMCID: PMC4337228 DOI: 10.1186/s12936-015-0597-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/30/2015] [Indexed: 11/28/2022] Open
Abstract
Background The World Health Organization (WHO) recommends parasitologic confirmation of suspected malaria cases before treatment. Due to the limited availability of quality microscopy services, this recommendation has become scalable following increased use of antigen-detecting malaria rapid diagnostic tests (RDTs) in many malaria-endemic countries. This study was carried out to monitor quality of RDT performance in selected health facilities using two quality assurance (QA) methods: reference microscopy and detection of parasite DNA by real-time quantitative polymerase chain reaction (qPCR) on dried blood spots (DBS). Methods Blood samples for QA were collected from patients undergoing RDT for diagnostic confirmation of malaria during two to three consecutive days per month in 12 health facilities in rural Tanzania. Stained blood smears (BS) were first examined at the district hospitals (BS1) and then at a reference laboratory (BS2). Discordant BS1 and BS2 results prompted a third examination. Molecular analysis was carried out at the Ifakara Health Institute laboratory in Bagamoyo. Results Malaria RDTs had a higher positivity rate (6.5%) than qPCR (4.2%) or microscopy (2.9% for BS1 and 2.5% for BS2). Poor correlation was observed between RDT and BS results: BS1 (K = 0.5), BS2 (K = 0.43) and qPCR (K = 0.45), challenging the utility of these tests for RDT QA. In addition, many challenges related to qPCR processing were recorded and long delays in obtaining QA test results for both microscopy and qPCR. Conclusions Overall there was limited agreement among the three diagnostic approaches and neither microscopy nor qPCR appear to be good QA options for RDTs under field conditions.
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Affiliation(s)
- Irene M Masanja
- Health System Sciences, Ifakara Health Institute, PO Box 78373, Dar es Salaam, Tanzania.
| | - Meredith L McMorrow
- Malaria Branch, Centers for Global Health, US Centers for Disease Control and Prevention, Atlanta, GA, USA. .,US Public Health Services, Rockville, Maryland, USA.
| | - Mussa B Maganga
- Health System Sciences, Ifakara Health Institute, PO Box 78373, Dar es Salaam, Tanzania.
| | - Debora Sumari
- Health System Sciences, Ifakara Health Institute, PO Box 78373, Dar es Salaam, Tanzania.
| | - Venkatachalam Udhayakumar
- Malaria Branch, Centers for Global Health, US Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Peter D McElroy
- Malaria Branch, Centers for Global Health, US Centers for Disease Control and Prevention, Atlanta, GA, USA. .,US President Malaria Initiative (PMI), Dar es Salaam, United Republic of Tanzania.
| | - S Patrick Kachur
- Malaria Branch, Centers for Global Health, US Centers for Disease Control and Prevention, Atlanta, GA, USA. .,US Public Health Services, Rockville, Maryland, USA.
| | - Naomi W Lucchi
- Malaria Branch, Centers for Global Health, US Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Faye B, Nath-Chowdhury M, Tine RC, Ndiaye JL, Sylla K, Camargo FW, Martel N, Foly K, Lô AC, Abiola A, Sow D, Ndiaye M, Ndiaye D, Ndao M, Gaye O. Accuracy of HRP2 RDT (Malaria Antigen P.f®) compared to microscopy and PCR for malaria diagnosis in Senegal. Pathog Glob Health 2014; 107:273-8. [PMID: 23916337 DOI: 10.1179/2047773213y.0000000102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Rapid diagnosis tests (RDTs) allow for the confirmation of malaria diagnosis. In Senegal, RDTs detecting HRP2 have been adopted in 2008 for malaria diagnosis. However, the sustainability of this strategy requires adequate and regular quality control. PCR on DNA extracted in nitrocellulose band of RDTs enable quality control. A RDT (Malaria Antigen P.f®) and a thick smear were performed on patients with suspected malaria. DNA was extracted from the nitrocellulose band of RDTs to which a non-specific PCR and a specific PCR were applied. The results of the RDT were compared with those obtained from the thick smear and the PCR to measure sensitivity, specificity as well as positive and negative predictive values. For 81.6% of the 273 patients involved, the thick smear was positive. Rapid diagnosis tests were positive for 85.7% of the patients. Non-specific PCR was positive on 87.9% of RDTs. Plasmodium falciparum was found in 99.5% of patients and Plasmodium ovale appeared in only 0.4% of patients. Sensitivity of the Malaria Antigen Pf® RDT in relation to thick smear and to PCR was 98.2% and 97.1% respectively. Quality control with PCR on the nitrocellulose band performed several months after it was used confirms its adequate level of sensitivity. The collection and screening of DNA present in already used RDT is a good means of quality control for this tool. It is also a relevant alternative to the molecular approach in the context of a reduction in the transmission of malaria.
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Affiliation(s)
- Babacar Faye
- University Cheikh Anta Diop, Avenue Cheikh Anta Diop, Dakar, Senegal.
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29
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Lo AC, Faye B, Ba EH, Cisse B, Tine R, Abiola A, Ndiaye M, Ndiaye JLA, Ndiaye D, Sokhna C, Gomis JF, Dieng Y, Faye O, Ndir O, Milligan P, Cairns M, Hallett R, Sutherland C, Gaye O. Prevalence of molecular markers of drug resistance in an area of seasonal malaria chemoprevention in children in Senegal. Malar J 2013; 12:137. [PMID: 23617576 PMCID: PMC3652725 DOI: 10.1186/1475-2875-12-137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/07/2013] [Indexed: 11/23/2022] Open
Abstract
Background In sub-Saharan Africa, malaria is the leading cause of morbidity and mortality especially in children. In Senegal, seasonal malaria chemoprevention (SMC) previously referred to as intermittent preventive treatment in children (IPTc) is a new strategy for malaria control in areas of high seasonal transmission. An effectiveness study of SMC, using sulphadoxine-pyrimethamine (SP) plus amodiaquine (AQ), was conducted in central Senegal from 2008 to 2010 to obtain information about safety, feasibility of delivery, and cost effectiveness of SMC. Here are report the effect of SMC delivery on the prevalence of markers of resistance to SP and AQ. Methods This study was conducted in three health districts in Senegal with 54 health posts with a gradual introduction of SMC. Three administrations of the combination AQ + SP were made during the months of September, October and November of each year in children aged less than 10 years living in the area. Children were surveyed in December of each year and samples (filter paper and thick films) were made in 2008, 2009 and 2010. The prevalence of mutations in the pfdhfr, pfdhps, pfmdr1 and pfcrt genes was investigated by sequencing and RTPCR in samples positive by microscopy for Plasmodium falciparum. Results Mutations at codon 540 of pfdhps and codon 164 of pfdhfr were not detected in the study. Among children with parasitaemia at the end of the transmission seasons, the CVIET haplotypes of pfcrt and the 86Y polymorphism of pfmdr1 were more common among those that had received SMC, but the number of infections detected was very low and confidence intervals were wide. The overall prevalence of these mutations was lower in SMC areas than in control areas, reflecting the lower prevalence of parasitaemia in areas where SMC was delivered. Conclusion The sensitivity of P. falciparum to SMC drugs should be regularly monitored in areas deploying this intervention. Overall the prevalence of genotypes associated with resistance to either SP or AQ was lower in SMC areas due to the reduced number of parasitaemia individuals.
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Affiliation(s)
- Aminata C Lo
- Service of Parasitology, Faculty of Medicine, University Cheikh Anta Diop, Dakar, Senegal.
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30
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Morris U, Aydin-Schmidt B, Shakely D, Mårtensson A, Jörnhagen L, Ali AS, Msellem MI, Petzold M, Gil JP, Ferreira PE, Björkman A. Rapid diagnostic tests for molecular surveillance of Plasmodium falciparum malaria -assessment of DNA extraction methods and field applicability. Malar J 2013; 12:106. [PMID: 23510231 PMCID: PMC3605315 DOI: 10.1186/1475-2875-12-106] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/10/2013] [Indexed: 11/20/2022] Open
Abstract
Background The need for new malaria surveillance tools and strategies is critical, given improved global malaria control and regional elimination efforts. High quality Plasmodium falciparum DNA can reliably be extracted from malaria rapid diagnostic tests (RDTs). Together with highly sensitive molecular assays, wide scale collection of used RDTs may serve as a modern tool for improved malaria case detection and drug resistance surveillance. However, comparative studies of DNA extraction efficiency from RDTs and the field applicability are lacking. The aim of this study was to compare and evaluate different methods of DNA extraction from RDTs and to test the field applicability for the purpose of molecular epidemiological investigations. Methods DNA was extracted from two RDT devices (Paracheck-Pf® and SD Bioline Malaria Pf/Pan®), seeded in vitro with 10-fold dilutions of cultured 3D7 P. falciparum parasites diluted in malaria negative whole blood. The level of P. falciparum detection was determined for each extraction method and RDT device with multiple nested-PCR and real-time PCR assays. The field applicability was tested on 855 paired RDT (Paracheck-Pf) and filter paper (Whatman® 3MM) blood samples (734 RDT negative and 121 RDT positive samples) collected from febrile patients in Zanzibar 2010. RDT positive samples were genotyped at four key single nucleotide polymorphisms (SNPs) in pfmdr1 and pfcrt as well as for pfmdr1 copy number, all associated with anti-malarial drug resistance. Results The P. falciparum DNA detection limit varied with RDT device and extraction method. Chelex-100 extraction performed best for all extraction matrixes. There was no statistically significant difference in PCR detection rates in DNA extracted from RDTs and filter paper field samples. Similarly there were no significant differences in the PCR success rates and genotyping outcomes for the respective SNPs in the 121 RDT positive samples. Conclusions The results support RDTs as a valuable source of parasite DNA and provide evidence for RDT-DNA extraction for improved malaria case detection, molecular drug resistance surveillance, and RDT quality control.
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Affiliation(s)
- Ulrika Morris
- Malaria Research, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.
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31
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Sturrock HJW, Hsiang MS, Cohen JM, Smith DL, Greenhouse B, Bousema T, Gosling RD. Targeting asymptomatic malaria infections: active surveillance in control and elimination. PLoS Med 2013; 10:e1001467. [PMID: 23853551 PMCID: PMC3708701 DOI: 10.1371/journal.pmed.1001467] [Citation(s) in RCA: 246] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hugh Sturrock and colleagues discuss the role of active case detection in low malaria transmission settings. They argue that the evidence for its effectiveness is sparse and that targeted mass drug administration should be evaluated as an alternative or addition to active case detection. Please see later in the article for the Editors' Summary
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Affiliation(s)
- Hugh J W Sturrock
- Malaria Elimination Initiative, Global Health Group, University of California, San Francisco, USA.
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Piedade R, Gil JP. The pharmacogenetics of antimalaria artemisinin combination therapy. Expert Opin Drug Metab Toxicol 2011; 7:1185-200. [PMID: 21899476 DOI: 10.1517/17425255.2011.608660] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Plasmodium falciparum malaria is one of the world's most lethal infectious diseases, commanding millions of drug administrations per year. The pharmacogenetics of these drugs is poorly known, although its application can be pivotal for the optimized management of this disease. AREAS COVERED The main components of artemisinin combination therapy (ACT), the worldwide main antimalarial strategy, are metabolized by the polymorphic CYP3A4 (mefloquine, artemether, lumefantrine), CYP2C8 (amodiaquine), CYP2A6 (artesunate) and CYP1A1/2 (amodiaquine/desethylamodiaquine), with dihydroartemisinin being acted by Phase II UDP-glucuronosyltransferases. The worldwide adoption of ACT is leading to a large number of antimalarial treatments. Simultaneously, the feared development of parasite drug resistance might drive dosing increases. In these scenarios of increased drug exposure, pharmacogenetics can be a key tool supporting evidence-based medicine aiming for the longest possible useful lifespan of this important chemotherapy. EXPERT OPINION Translation in this moment is not operationally possible at an individual level, but large population studies are achievable for: i) the development of robust pharmacogenetics markers; and ii) the parallel development of a pharmacogenetic cartography of malaria settings. Advances in the understanding of antimalarial pharmacogenetics are urgent in order to protect the exposed populations, enhance the effectiveness of ACT and, consequently, contributing for the long aimed elimination of the disease.
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Affiliation(s)
- Rita Piedade
- Karolinska Institute, Division of Pharmacogenetics, Department of Physiology and Pharmacology, Stockholm, Sweden
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Cnops L, Boderie M, Gillet P, Van Esbroeck M, Jacobs J. Rapid diagnostic tests as a source of DNA for Plasmodium species-specific real-time PCR. Malar J 2011; 10:67. [PMID: 21435256 PMCID: PMC3075219 DOI: 10.1186/1475-2875-10-67] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 03/24/2011] [Indexed: 11/25/2022] Open
Abstract
Background This study describes the use of malaria rapid diagnostic tests (RDTs) as a source of DNA for Plasmodium species-specific real-time PCR. Methods First, the best method to recover DNA from RDTs was investigated and then the applicability of this DNA extraction method was assessed on 12 different RDT brands. Finally, two RDT brands (OptiMAL Rapid Malaria Test and SDFK60 malaria Ag Plasmodium falciparum/Pan test) were comprehensively evaluated on a panel of clinical samples submitted for routine malaria diagnosis at ITM. DNA amplification was done with the 18S rRNA real-time PCR targeting the four Plasmodium species. Results of PCR on RDT were compared to those obtained by PCR on whole blood samples. Results Best results were obtained by isolating DNA from the proximal part of the nitrocellulose component of the RDT strip with a simple DNA elution method. The PCR on RDT showed a detection limit of 0.02 asexual parasites/μl, which was identical to the same PCR on whole blood. For all 12 RDT brands tested, DNA was detected except for one brand when a low parasite density sample was applied. In RDTs with a plastic seal covering the nitrocellulose strip, DNA extraction was hampered. PCR analysis on clinical RDT samples demonstrated correct identification for single species infections for all RDT samples with asexual parasites of P. falciparum (n = 60), Plasmodium vivax (n = 10), Plasmodium ovale (n = 10) and Plasmodium malariae (n = 10). Samples with only gametocytes were detected in all OptiMAL and in 10 of the 11 SDFK60 tests. None of the negative samples (n = 20) gave a signal by PCR on RDT. With PCR on RDT, higher Ct-values were observed than with PCR on whole blood, with a mean difference of 2.68 for OptiMAL and 3.53 for SDFK60. Mixed infections were correctly identified with PCR on RDT in 4/5 OptiMAL tests and 2/5 SDFK60 tests. Conclusions RDTs are a reliable source of DNA for Plasmodium real-time PCR. This study demonstrates the best method of RDT fragment sampling for a wide range of RDT brands in combination with a simple and low cost extraction method, allowing RDT quality control.
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Affiliation(s)
- Lieselotte Cnops
- Department of Clinical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium.
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