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  1. Article ; Online: Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing.

    Levine, Zoë C / Sene, Aita / Mkandawire, Winnie / Deme, Awa B / Ndiaye, Tolla / Sy, Mouhamad / Gaye, Amy / Diedhiou, Younouss / Mbaye, Amadou M / Ndiaye, Ibrahima M / Gomis, Jules / Ndiop, Médoune / Sene, Doudou / Faye Paye, Marietou / MacInnis, Bronwyn L / Schaffner, Stephen F / Park, Daniel J / Badiane, Aida S / Colubri, Andres /
    Ndiaye, Mouhamadou / Sy, Ngayo / Sabeti, Pardis C / Ndiaye, Daouda / Siddle, Katherine J

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 747

    Abstract: The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical ... ...

    Abstract The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata in a cross-sectional study of febrile patients and healthy controls in a low malaria burden area. Using 16S and untargeted sequencing, we detected viral, bacterial, or eukaryotic pathogens in 23% (38/163) of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15.5% and 3.8% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model that can distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs (F1 score: 0.823). These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
    MeSH term(s) Humans ; Senegal/epidemiology ; Cross-Sectional Studies ; Malaria/diagnosis ; Malaria/epidemiology ; Plasmodium ; Fever/epidemiology ; Borrelia/genetics
    Language English
    Publishing date 2024-01-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-44800-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Improving diagnosis of non-malarial fevers in Senegal:

    Levine, Zoë C / Sene, Aita / Mkandawire, Winnie / Deme, Awa B / Ndiaye, Tolla / Sy, Mouhamad / Gaye, Amy / Diedhiou, Younouss / Mbaye, Amadou M / Ndiaye, Ibrahima / Gomis, Jules / Ndiop, Médoune / Sene, Doudou / Paye, Marietou Faye / MacInnis, Bronwyn / Schaffner, Stephen F / Park, Daniel J / Badiane, Aida S / Colubri, Andres /
    Ndiaye, Mouhamadou / Sy, Ngayo / Sabeti, Pardis C / Ndiaye, Daouda / Siddle, Katherine J

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical ... ...

    Abstract The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata from febrile patients and healthy controls in a low malaria burden area. Using 16S and unbiased sequencing, we detected viral, bacterial, or eukaryotic pathogens in 29% of NMFI cases. Bacteria were the most common, with relapsing fever
    Language English
    Publishing date 2023-08-25
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.08.24.23294564
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Evaluating the performance of Plasmodium falciparum genetic metrics for inferring National Malaria Control Programme reported incidence in Senegal.

    Wong, Wesley / Schaffner, Stephen F / Thwing, Julie / Seck, Mame Cheikh / Gomis, Jules / Diedhiou, Younouss / Sy, Ngayo / Ndiop, Medoune / Ba, Fatou / Diallo, Ibrahima / Sene, Doudou / Diallo, Mamadou Alpha / Ndiaye, Yaye Die / Sy, Mouhamad / Sene, Aita / Sow, Djiby / Dieye, Baba / Tine, Abdoulaye / Ribado, Jessica /
    Suresh, Joshua / Lee, Albert / Battle, Katherine E / Proctor, Joshua L / Bever, Caitlin A / MacInnis, Bronwyn / Ndiaye, Daouda / Hartl, Daniel L / Wirth, Dyann F / Volkman, Sarah K

    Malaria journal

    2024  Volume 23, Issue 1, Page(s) 68

    Abstract: Background: Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programmes (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) ... ...

    Abstract Background: Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programmes (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence.
    Methods: This study examined parasites from 3147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, a series of Poisson generalized linear mixed-effects models were constructed to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates.
    Results: Model-predicted incidence was compared with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (< 10/1000/annual [‰]).
    Conclusions: When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence > 10‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was < 10‰, many of the correlations between parasite genetics and incidence were reversed, which may reflect the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low.
    MeSH term(s) Humans ; Senegal/epidemiology ; Incidence ; Plasmodium falciparum/genetics ; Superinfection ; Malaria
    Language English
    Publishing date 2024-03-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2091229-8
    ISSN 1475-2875 ; 1475-2875
    ISSN (online) 1475-2875
    ISSN 1475-2875
    DOI 10.1186/s12936-024-04897-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal.

    Schaffner, Stephen F / Badiane, Aida / Khorgade, Akanksha / Ndiop, Medoune / Gomis, Jules / Wong, Wesley / Ndiaye, Yaye Die / Diedhiou, Younouss / Thwing, Julie / Seck, Mame Cheikh / Early, Angela / Sy, Mouhamad / Deme, Awa / Diallo, Mamadou Alpha / Sy, Ngayo / Sene, Aita / Ndiaye, Tolla / Sow, Djiby / Dieye, Baba /
    Ndiaye, Ibrahima Mbaye / Gaye, Amy / Ndiaye, Aliou / Battle, Katherine E / Proctor, Joshua L / Bever, Caitlin / Fall, Fatou Ba / Diallo, Ibrahima / Gaye, Seynabou / Sene, Doudou / Hartl, Daniel L / Wirth, Dyann F / MacInnis, Bronwyn / Ndiaye, Daouda / Volkman, Sarah K

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 7268

    Abstract: We here analyze data from the first year of an ongoing nationwide program of genetic surveillance of Plasmodium falciparum parasites in Senegal. The analysis is based on 1097 samples collected at health facilities during passive malaria case detection in ...

    Abstract We here analyze data from the first year of an ongoing nationwide program of genetic surveillance of Plasmodium falciparum parasites in Senegal. The analysis is based on 1097 samples collected at health facilities during passive malaria case detection in 2019; it provides a baseline for analyzing parasite genetic metrics as they vary over time and geographic space. The study's goal was to identify genetic metrics that were informative about transmission intensity and other aspects of transmission dynamics, focusing on measures of genetic relatedness between parasites. We found the best genetic proxy for local malaria incidence to be the proportion of polygenomic infections (those with multiple genetically distinct parasites), although this relationship broke down at low incidence. The proportion of related parasites was less correlated with incidence while local genetic diversity was uninformative. The type of relatedness could discriminate local transmission patterns: two nearby areas had similarly high fractions of relatives, but one was dominated by clones and the other by outcrossed relatives. Throughout Senegal, 58% of related parasites belonged to a single network of relatives, within which parasites were enriched for shared haplotypes at known and suspected drug resistance loci and at one novel locus, reflective of ongoing selection pressure.
    MeSH term(s) Animals ; Humans ; Parasites ; Malaria, Falciparum/epidemiology ; Malaria, Falciparum/parasitology ; Senegal/epidemiology ; Malaria/epidemiology ; Plasmodium falciparum/genetics
    Language English
    Publishing date 2023-11-10
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-43087-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal.

    Schaffner, Stephen F / Badiane, Aida / Khorgade, Akanksha / Ndiop, Medoune / Gomis, Jules / Wong, Wesley / Ndiaye, Yaye Die / Diedhiou, Younouss / Thwing, Julie / Seck, Mame Cheikh / Early, Angela / Sy, Mouhamad / Deme, Awa / Diallo, Mamadou Alpha / Sy, Ngayo / Sene, Aita / Ndiaye, Tolla / Sow, Djiby / Dieye, Baba /
    Ndiaye, Ibrahima Mbaye / Gaye, Amy / Ndiaye, Aliou / Battle, Katherine E / Proctor, Joshua L / Bever, Caitlin / Fall, Fatou Ba / Diallo, Ibrahima / Gaye, Seynabou / Sene, Doudou / Hartl, Daniel L / Wirth, Dyann F / MacInnis, Bronwyn / Ndiaye, Daouda / Volkman, Sarah K

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: Parasite genetic surveillance has the potential to play an important role in malaria control. We describe here an analysis of data from the first year of an ongoing, nationwide program of genetic surveillance ... ...

    Abstract Parasite genetic surveillance has the potential to play an important role in malaria control. We describe here an analysis of data from the first year of an ongoing, nationwide program of genetic surveillance of
    Language English
    Publishing date 2023-05-30
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.11.23288401
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Two decades of molecular surveillance in Senegal reveal changes in known drug resistance mutations associated with historical drug use and seasonal malaria chemoprevention.

    Ndiaye, Yaye Die / Wong, Wesley / Thwing, Julie / Schaffner, Stephen S / Tine, Abdoulaye / Diallo, Mamadou Alpha / Deme, Awa / Sy, Mouhammad / Bei, Amy K / Thiaw, Alphonse B / Daniels, Rachel / Ndiaye, Tolla / Gaye, Amy / Ndiaye, Ibrahima Mbaye / Toure, Mariama / Gadiaga, Nogaye / Sene, Aita / Sow, Djiby / Garba, Mamane N /
    Yade, Mamadou Samba / Dieye, Baba / Diongue, Khadim / Zoumarou, Daba / Ndiaye, Aliou / Gomis, Jules / Fall, Fatou Ba / Ndiop, Medoune / Diallo, Ibrahima / Sene, Doudou / Macinnis, Bronwyn / Seck, Mame Cheikh / Ndiaye, Mouhamadou / Badiane, Aida S / Hartl, Daniel L / Volkman, Sarah K / Wirth, Dyann F / Ndiaye, Daouda

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: Drug resistance ... ...

    Abstract Drug resistance in
    Language English
    Publishing date 2023-04-26
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.24.23288820
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Inter-library loan at ZB MED

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  7. Article: Evaluating the performance of Plasmodium falciparum genetics for inferring National Malaria Control Program reported incidence in Senegal.

    Wong, Wesley / Schaffner, Stephen F / Thwing, Julie / Seck, Mame Cheikh / Gomis, Jules / Diedhiou, Younouss / Sy, Ngayo / Ndiop, Medoune / Ba, Fatou / Diallo, Ibrahima / Sene, Doudou / Diallo, Mamadou Alpha / Ndiaye, Yaye Die / Sy, Mouhamad / Sene, Aita / Sow, Djiby / Dieye, Baba / Tine, Abdoulaye / Ribado, Jessica /
    Suresh, Joshua / Lee, Albert / Battle, Katherine E / Proctor, Joshua L / Bever, Caitlin A / MacInnis, Bronwyn / Ndiaye, Daouda / Hartl, Daniel L / Wirth, Dyann F / Volkman, Sarah K

    Research square

    2023  

    Abstract: Genetic surveillance of ... ...

    Abstract Genetic surveillance of the
    Language English
    Publishing date 2023-11-01
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-3516287/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Quality assessment of malaria microscopic diagnosis at the Aristide Le Dantec University Hospital of Dakar, Senegal, in 2020.

    Garba, Mamane N / Dème, Awa B / Diongue, Khadim / Diédhiou, Younousse / Mbaye, Amadou M / Dia, NDèye M / Seck, N'Dèye A / Zoumarou, Daba / Ndiaye, Lamine / Yade, Mamadou S / Dièye, Baba / Sène, Aita / Tine, Abdoulaye / Touré, Mariama / Gadiaga, Nogaye / Fall, Awa / Ngom, Bassirou / Sow, Djiby / Ndiaye, Aliou /
    Keita, Astou / Ndiaye, Mame F / Gomis, Jules F / Diop, Nana F / Diallo, Guète / Ndiaye, Ibrahima M / Ba, Elhadj M / Bitèye, Omar / Ndiaye, Cheikh / Mbodji, Fama S D / Ndiaye, Pape O / Ndiaye, Tolla / Gaye, Amy / Sy, Mouhamad / Ndiaye, Yaye D / Seck, Mame C / Ndiaye, Mouhamadou / Badiane, Aida S / Diallo, Mamadou A / Ndiaye, Daouda

    BMC research notes

    2024  Volume 17, Issue 1, Page(s) 68

    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 ... ...

    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.
    MeSH term(s) Humans ; Senegal ; Reproducibility of Results ; Malaria/diagnosis ; Malaria/parasitology ; Laboratories ; Hospitals, University
    Language English
    Publishing date 2024-03-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2413336-X
    ISSN 1756-0500 ; 1756-0500
    ISSN (online) 1756-0500
    ISSN 1756-0500
    DOI 10.1186/s13104-023-06571-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018.

    Gaye, Amy / Ndiaye, Tolla / Sy, Mouhamad / Deme, Awa B / Thiaw, Alphonse B / Sene, Aita / Ndiaye, Cheikh / Diedhiou, Younouss / Mbaye, Amadou M / Ndiaye, Ibrahima / Tomkins-Tinch, Christopher / Gomis, Jules F / Badiane, Aida S / MacInnis, Bronwyn / Park, Daniel J / Ndiaye, Mouhamadou / Sy, Ngayo / Sabeti, Pardis C / Siddle, Katherine J /
    Ndiaye, Daouda

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 10321

    Abstract: Dengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is known about the ... ...

    Abstract Dengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is known about the genetic diversity of dengue virus (DENV) in Senegal. Here we report complete viral genomes from 17 previously undetected DENV cases from the city of Thiès. In total we identified 19 cases of DENV in a cohort of 198 individuals with fever collected in October and November 2018. We detected 3 co-circulating serotypes; DENV 3 was the most frequent accounting for 11/17 sequences (65%), 4 (23%) were DENV2 and 2 (12%) were DENV1. Sequences were most similar to recent sequences from West Africa, suggesting ongoing local circulation of viral populations; however, detailed inference is limited by the scarcity of available genomic data. We did not find clear associations with reported clinical signs or symptoms, highlighting the importance of testing for diagnosing febrile diseases. Overall, these findings expand the known range of DENV in Senegal, and underscore the need for better genomic characterization of DENV in West Africa.
    MeSH term(s) Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; DNA, Viral/isolation & purification ; Dengue/blood ; Dengue/diagnosis ; Dengue/epidemiology ; Dengue/virology ; Dengue Virus/genetics ; Dengue Virus/isolation & purification ; Disease Outbreaks/statistics & numerical data ; Female ; Genome, Viral ; Humans ; Male ; Middle Aged ; Molecular Epidemiology ; Phylogeny ; Senegal/epidemiology ; Serogroup ; Young Adult
    Chemical Substances DNA, Viral
    Language English
    Publishing date 2021-05-14
    Publishing country England
    Document type Journal Article ; Observational Study ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-89070-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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