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Garba MN, Dème AB, Diongue K, Diédhiou Y, Mbaye AM, Dia NDM, Seck NA, Zoumarou D, Ndiaye L, Yade MS, Dièye B, Sène A, Tine A, Touré M, Gadiaga N, Fall A, Ngom B, Sow D, Ndiaye A, Keita A, Ndiaye MF, Gomis JF, Diop NF, Diallo G, Ndiaye IM, Ba EM, Bitèye O, Ndiaye C, Mbodji FSD, Ndiaye PO, Ndiaye T, Gaye A, Sy M, Ndiaye YD, Seck MC, Ndiaye M, Badiane AS, Diallo MA, Ndiaye D. Quality assessment of malaria microscopic diagnosis at the Aristide Le Dantec University Hospital of Dakar, Senegal, in 2020. BMC Res Notes 2024; 17:68. [PMID: 38461329 PMCID: PMC10925005 DOI: 10.1186/s13104-023-06571-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/12/2023] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Following WHO guidelines, microscopy is the gold standard for malaria diagnosis in endemic countries. The Parasitology-Mycology laboratory (LPM) is the National Reference Laboratory and is currently undergoing ISO 15189 accreditation. In this context, we assessed the performance of the laboratory by confirming the reliability and the accuracy of results obtained in accordance with the requirements of the ISO 15189 standards. This study aimed to verify the method of microscopic diagnosis of malaria at the LPM, in the Aristide Le Dantec hospital (HALD) in Dakar, Senegal. METHODS This is a validation/verification study conducted from June to August 2020. Twenty (20) microscopic slides of thick/thin blood smear with known parasite densities (PD) selected from the Cheick Anta Diop University malaria slide bank in Dakar were used for this assessment. Six (6) were used to assess microscopists' ability to determine PD and fourteen (14) slides were used for detection (positive vs negative) and identification of parasites. Four (4) LPM-HALD microscopists read and recorded their results on prepared sheets. Data analysis was done with Microsoft Excel 2010 software. RESULTS A minimum threshold of 50% concordance was used for comparison. Of the twenty (20) slides read, 100% concordance was obtained on eight (8) detection (positive vs negative) slides. Four (4) out of the six (6) parasite density evaluation slides obtained a concordance of less than 50%. Thirteen (13) out of the fourteen (14) identification slides obtained a concordance greater than 50%. Only one (1) identification slide obtained zero agreement from the microscopists. For species identification a concordance greater than 80% was noted and the microscopists obtained scores between 0.20 and 0.4 on a scale of 0 to 1 for parasite density reading. The microscopists obtained 100% precision, sensitivity, specificity and both negative and positive predictive values. CONCLUSION This work demonstrated that the microscopic method of malaria diagnosis used in the LPM/HALD is in accordance with the requirements of WHO and ISO 15189. Further training of microscopists may be needed to maintain competency.
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Affiliation(s)
- Mamane N Garba
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal.
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal.
| | - Awa B Dème
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Khadim Diongue
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Younousse Diédhiou
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Amadou M Mbaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - NDèye M Dia
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - N'Dèye A Seck
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Daba Zoumarou
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Lamine Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Mamadou S Yade
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Baba Dièye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Aita Sène
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Abdoulaye Tine
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Mariama Touré
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Nogaye Gadiaga
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Awa Fall
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Bassirou Ngom
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Djiby Sow
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Aliou Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Astou Keita
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Mame F Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Jules F Gomis
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Nana F Diop
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Guète Diallo
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Ibrahima M Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Elhadj M Ba
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Omar Bitèye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Cheikh Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Fama S D Mbodji
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Pape O Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Tolla Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Amy Gaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Mouhamad Sy
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Yaye D Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Mame C Seck
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Mouhamadou Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Aida S Badiane
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Mamadou A Diallo
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Daouda Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Dakar, Senegal
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
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Ndiaye YD, Wong W, Thwing J, Schaffner SS, Tine A, Diallo MA, Deme A, Sy M, Bei AK, Thiaw AB, Daniels R, Ndiaye T, Gaye A, Ndiaye IM, Toure M, Gadiaga N, Sene A, Sow D, Garba MN, Yade MS, Dieye B, Diongue K, Zoumarou D, Ndiaye A, Gomis J, Fall FB, Ndiop M, Diallo I, Sene D, Macinnis B, Seck MC, Ndiaye M, Badiane AS, Hartl DL, Volkman SK, Wirth DF, Ndiaye D. Two decades of molecular surveillance in Senegal reveal changes in known drug resistance mutations associated with historical drug use and seasonal malaria chemoprevention. medRxiv 2023:2023.04.24.23288820. [PMID: 37163114 PMCID: PMC10168519 DOI: 10.1101/2023.04.24.23288820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Drug resistance in Plasmodium falciparum is a major threat to malaria control efforts. We analyzed data from two decades (2000-2020) of continuous molecular surveillance of P. falciparum parasite strains in Senegal to determine how historical changes in drug administration policy may have affected parasite evolution. We profiled several known drug resistance markers and their surrounding haplotypes using a combination of single nucleotide polymorphism (SNP) molecular surveillance and whole-genome sequence (WGS) based population genomics. We observed rapid changes in drug resistance markers associated with the withdrawal of chloroquine and introduction of sulfadoxine-pyrimethamine in 2003. We also observed a rapid increase in Pfcrt K76T and decline in Pfdhps A437G starting in 2014, which we hypothesize may reflect changes in resistance or fitness caused by seasonal malaria chemoprevention (SMC). Parasite populations evolve rapidly in response to drug use, and SMC preventive efficacy should be closely monitored.
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Affiliation(s)
- Yaye Die Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
| | - Julie Thwing
- Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA ,30329, USA
| | - Stephen S Schaffner
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Abdoulaye Tine
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mamadou Alpha Diallo
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Awa Deme
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mouhammad Sy
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Amy K Bei
- Yale School of Public Health, 60 College St, New Haven, CT 06510
| | - Alphonse B Thiaw
- Department of biochemistry and Functional Genomics, Sherbrooke University, 2500 Bd de l'Universite, Sherbrooke, QC J1K 2R1, Canada
| | - Rachel Daniels
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester MA 01605
| | - Tolla Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Amy Gaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Ibrahima Mbaye Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mariama Toure
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Nogaye Gadiaga
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Aita Sene
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Djiby Sow
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mamane N Garba
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mamadou Samba Yade
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Baba Dieye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Khadim Diongue
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Daba Zoumarou
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Aliou Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Jules Gomis
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Fatou Ba Fall
- Yale School of Public Health, 60 College St, New Haven, CT 06510
| | - Medoune Ndiop
- National Malaria Control Program (NMCP), Rue FN 20, Dakar 25270, Senegal
| | - Ibrahima Diallo
- National Malaria Control Program (NMCP), Rue FN 20, Dakar 25270, Senegal
| | - Doudou Sene
- National Malaria Control Program (NMCP), Rue FN 20, Dakar 25270, Senegal
| | - Bronwyn Macinnis
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Mame Cheikh Seck
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Mouhamadou Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Aida S Badiane
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138 USA
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
- Simmons University, 300 The Fenway, Boston, MA, 02115, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Daouda Ndiaye
- International Research Training Center on Genomics and Health Surveillance (CIGASS), Cheikh Anta Diop University, Dakar, 16477, Senegal
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA, 02115, USA
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