Current routine diagnosis of a life-threatening central nervous system (CNS) infections is based on commercial multiplex real-time PCR (RT-PCR) and in-vitro culture investigations, targeting a limited number of pathogens, which requires implementation of a universal diagnosis at the point-of-care laboratory. This study aimed to document a case of non-routinely diagnosed meningoencephalitis in a twelve-year-old patient in Niger Republic. Metagenomic-based on real-time sequencing was applied directly on DNA/RNA extracted from 50 µL leftover CSF sample using Oxford Nanopore MinION, to detect all residual microorganisms non-routinely targeted by RT-PCR panel. In parallel, 1 ng DNA/RNA was used for paired-end Illumina library preparation to confirm the MinION results. Real-time analysis of MinION data detected 132 WU Polyomavirus specific reads after one-hour run. Blast nucleotide of the fasta sequences after assembly of both Illumina and Nanopore reads against NCBI GenBank database identified WU polyomavirus strain W33 (GenBank accession no: GU296367.1). Haemophilus influenzae specific reads (667 reads) were detected which explains the possible co-infection bacteria-DNA virus in this case. Blastn after total reads assembly identified H. influenzae strain PittGG (GenBank accession n° CP000672), belonging to the non-typable H. influenzae genotype by muti-locus-sequence-typing analysis. Furthermore, Achromobacter xylosoxidans (599 reads) were detected in this patient. Based on these findings, we classified this case as polymicrobial meningoencephalitis. Using RT-mNGS, the pathogen genome could be detected directly from a clinical sample, with no specific target. This technique seems to be an adapted method to diagnose non-routinely detectable pathogens, as well as their genotype and antimicrobial susceptibility in reduced time.

This study aims to evaluate the factors influencing the adherence to the 2nd and 3rd doses during each cycle of seasonal malaria chemoprevention (SMC) in Burkina Faso, Mali, and Niger. Overall, 3,132 people were interviewed during surveys between 2019 and 2020 in 15 health districts. The median age was 30 years. In Burkina , Mali, and Niger, the proportions of non-adherence were 4.15% , 5.60%, and 13.30%, respectively (95% CI (-3.27% -0.37 %, p = 0.114 ) for the 2nd dose and 3.98%, 5.60% and 14.39% for the 3rd dose. The main cause of non-adherence to the 2nd and 3rd doses was other illnesses in 28.5% and 29.78% respectively in Burkina, 5.35% and 5.35% in Mali and 1.6% and 0.75% in Niger. It was followed by vomiting in 12.24% and 10.63% for Burkina and 2.45% and 3.78% in Niger. The last causes were refusal in 6.12% and 4.25% in Burkina , 33.9% and 15.25% in Mali and 0.8% and 1.51% in Niger. Non-adherence of doses related to parents was primary due to their absence in 28.5% and 27.65% in Burkina , 16.07% and 16.07% in Mali and 7.37 % and 6.06% in Niger. Travelling was the second cause in 12.24 % and 12.76% in Burkina , 19.64% and 19.64% in Mali and 0.81% and 0.75% in Niger. Non-adherence related to community distributors was mainly due to missing of the doses in 4.08% and 4.25% in Burkina , 23.21% and 23.21% in Mali, 77.04% and 76.51% in Niger. Our study reported very small proportions of non-adherence to 2nd and 3rd doses of SMC and identified the main causes of non-adherence.