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.

Despite global efforts to improve vaccination coverage, the number of zero dose and under immunized children has increased in the African continent, particularly in Nigeria where more than 2.3 million unvaccinated children currently reside, making it the country with highest number of unvaccinated children on the African continent. It is thus imperative to identity barriers and facilitators of immunization in Nigeria with a view to formulate and design targeted interventions that can effectively bridge the immunization gap in Nigeria. In this review, we systematically mapped and summarized existing literature and data on key barriers to vaccine uptake, and facilitators influencing immunization practices in Nigeria. The electronic databases were systematically searched and articles that reported determinants of routine immunization uptake in Nigeria from inception of the databases up till October 2023 were included. The eligible articles were evaluated using a set of pre-defined criteria and the extracted data were analysed and visualized. This scoping review identified barriers spanning logistical, socio-economic, cultural, and healthcare system-related aspects, highlighting the need for a multi-pronged approach to address these challenges. While considerable progress has been made over the years, persistent barriers like distance between area of residence of caregivers and immunization centers, vaccine shortages, poor interpersonal relationship between healthcare workers and caregivers and cultural/religious influences persist. Lastly, collaborative efforts among stakeholders and communities remain paramount in ensuring improved routine immunization coverage across the Nigeria’s diverse socio-cultural landscape.