Real-time metagenomics next-generation sequencing for diagnosing polymicrobial meningoencephalitis in Niger: A case report

Yacouba, Abdourahamane; Garba, Moumouni; Boubacar, Marou Soumana Boubacar; Saley, Sahada M; Aboubacar, Samaila; Ousmane, Abdoulaye; Olowo-Okere, Ahmed; Brah, Souleymane; Daou, Mamane; Doutchi, Mahamadou; Adehossi, Eric; Mamadou, Saidou; Morsli, Madjid

doi:10.21608/mid.2024.298520.2020

	Real-time metagenomics next-generation sequencing for diagnosing polymicrobial meningoencephalitis in Niger: A case report
Microbes and Infectious Diseases
Volume 6, Issue 4, November 2025, Pages 6402-6410 PDF (888.22 K)
Document Type: Short Reports (case reports)
DOI: 10.21608/mid.2024.298520.2020
Authors
Abdourahamane Yacouba^* ¹^{, 2}; Moumouni Garba¹^{, 2}; Marou Soumana Boubacar Boubacar¹^{, 3}; Sahada M Saley¹^{, 3}; Samaila Aboubacar¹^{, 2}; Abdoulaye Ousmane⁴; Ahmed Olowo-Okere⁵; Souleymane Brah¹^{, 2}; Mamane Daou¹^{, 3}; Mahamadou Doutchi⁶; Eric Adehossi¹^{, 7}; Saidou Mamadou¹^{, 2}; Madjid Morsli⁸
¹Faculté des Sciences de la Santé, Université Abdou Moumouni, PB 10896, Niamey, Niger
²Hôpital National Amirou Boubacar Diallo, PB 1364 Niamey, Niger
³Hôpital National de Niamey, PB 238 Niamey, Niger
⁴Faculté des Sciences de la Santé, Université Dan Dicko Dan Kolodo, PB 465 Maradi, Niger
⁵Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, University of Abuja, PB 2346 Abuja, Nigeria
⁶Faculté des Sciences de la Santé, Université André Salifou, PB 656 Zinder, Niger
⁷Hôpital Général de Référence, PB 12674 Niamey, Niger
⁸VBIC, INSERM U1047, Univ Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Cedex 9, 30029 Nîmes, France
Abstract
Background: Real-time metagenomics next-generation sequencing (RT-mNGS) has emerged as a high-throughput technique for directly identifying pathogen genomes from clinical samples. This study aimed to document a case of nonroutinely diagnosed meningoencephalitis using RT-mNGS in the Niger Republic. Case presentation: The patient was a 12-year-old African Nigerien female who reported fever for two weeks before she visited our hospital, as her fever had worsened with focal neurologic deficits. All other physical examinations yielded no notable findings or abnormalities. A brain abscess was first presumed in this patient and empirical treatment with ceftriaxone and metronidazole was initiated before diagnosis. Conventional bacteriological tests yielded negative results and the lesions seen on brain-computed tomography images are not specific for brain abscesses. Using real-time metagenomic next-generation sequencing (RT-mNGS), the pathogen's genomes were detected after a one-hour sequencing run, directly from leftover cerebrospinal fluid. WU polyomavirus strain W33 (GenBank accession no: GU296367.1) was identified in the patient’s sample. Haemophilus influenzae-specific reads (667 reads) were also detected, which explains the possible bacteria–DNA virus coinfection in this case. Furthermore, Achromobacter xylosoxidans (599 reads) was detected in this patient. Based on these findings, we classified this case as polymicrobial meningoencephalitis. Conclusion: This case report highlights the significance of RT-mNGS in diagnosing non-routinely detectable pathogens. RT-mNGS can rapidly and accurately characterize meningoencephalitis pathogen and might contribute to a reduction in mortality. However, the issue of sample contamination should always be addressed with high priority.
Keywords
Real-time metagenomics; meningoencephalitis; fever of unknown origin; Niger republic
Supplementary Files 24-Suppl.pdf
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