Genomic investigation of atypical malaria cases in Kanel, northern Senegal

Mamadou Alpha Diallo,Moustapha Cissé,Yaye Dié Ndiaye ,Alioune Badara Guèye ,Daouda Ndiaye,Mouhamad Sy,Bronwyn Macinnis,Dyann F Wirth,Amy Gaye,Awa B Déme ,Tolla Ndiaye,Mame Cheikh Seck,Khadim Diongue,Ibrahima Ndiaye ,Katherine J Siddle,Tamba Souané,Baba Dièye ,Yakhya Dièye ,Fatou Fall ,Doudou Sène,Sarah K Volkman,Aïda Sadikh Badiane

doi:10.1186/s12936-021-03637-x

Abstract

BackgroundThe diagnosis of malaria cases in regions where the malaria burden has decreased significantly and prevalence is very low is more challenging, in part because of reduced clinical presumption of malaria. The appearance of a cluster of malaria cases with atypical symptoms in Mbounguiel, a village in northern Senegal where malaria transmission is low, in September 2018 exemplifies this scenario. The collaboration between the National Malaria Control Programme (NMCP) at the Senegal Ministry of Health and the Laboratory of Parasitology and Mycology at Cheikh Anta Diop University worked together to evaluate this cluster of malaria cases using molecular and serological tools.MethodsMalaria cases were diagnosed primarily by rapid diagnostic test (RDT), and confirmed by photo-induced electron transfer-polymerase chain reaction (PET-PCR). 24 single nucleotide polymorphisms (SNPs) barcoding was used for Plasmodium falciparum genotyping. Unbiased metagenomic sequencing and Luminex-based multi-pathogen antibody and antigen profiling were used to assess exposure to other pathogens.ResultsNine patients, of 15 suspected cases, were evaluated, and all nine samples were found to be positive for P. falciparum only. The 24 SNPs molecular barcode showed the predominance of polygenomic infections, with identifiable strains being different from one another. All patients tested positive for the P. falciparum antigens. No other pathogenic infection was detected by either the serological panel or metagenomic sequencing.ConclusionsThis work, undertaken locally within Senegal as a collaboration between the NMCP and a research laboratory at University of Cheikh Anta Diop (UCAD) revealed that a cluster of malaria cases were caused by different strains of P. falciparum. The public health response in real time demonstrates the value of local molecular and genomics capacity in affected countries for disease control and elimination.

Highlights

The diagnosis of malaria cases in regions where the malaria burden has decreased significantly and prevalence is very low is more challenging, in part because of reduced clinical presumption of malaria
This study describe the molecular and serological investigation performed in partnership between health ministries, public health authorities and a research laboratory in Senegal to evaluate a cluster of atypical malaria cases in Kanel
Characteristics of patients A total of nine samples collected from the suspected cases were sent to the LPM at University of Cheikh Anta Diop (UCAD) for molecular confirmation

Summary

Introduction

The diagnosis of malaria cases in regions where the malaria burden has decreased significantly and prevalence is very low is more challenging, in part because of reduced clinical presumption of malaria. The clinical malaria cases reported here occurred in the village of Mbounguiel situated in the department of Kanel within the Matam region. The investigation takes place in the house of the index case and the five closest concessions within a radius of 100 m, within 24 h of the case being detected for clinical and socio-anthropological investigation, 72 h for parasitological investigation including molecular tools as well as entomological and environmental investigation. It is carried out by an investigative team [1]

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