Real-Time Metagenomics Next-Generation Sequencing for Diagnosing Polymicrobial Meningoencephalitis in Niger: A Case Report

Yacouba, Abdourahamane; Garba, Moumouni; Soumana, Boubacar M; 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
Articles in Press, Accepted Manuscript, Available Online from 04 August 2024
Document Type: Short Reports (case reports)
DOI: 10.21608/mid.2024.298520.2020
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Authors
Abdourahamane Yacouba ¹^{, 2}; Moumouni Garba¹^{, 2}; Boubacar M Soumana¹^{, 3}; Sahada M Saley⁴; Samaila Aboubacar⁵; Abdoulaye Ousmane ⁶; Ahmed Olowo-Okere ⁷; Souleymane Brah⁵; Mamane Daou⁵; Mahamadou Doutchi⁸; Eric Adehossi⁵; Saidou Mamadou ⁹; Madjid Morsli ¹⁰
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
⁴Department of medicine, Faculty of Health Sciences, Université Abdou Moumouni, Niamey, Niger
⁵Department of Medicine, Faculty of Health Sciences, Université Abdou Moumouni, Niamey, Niger
⁶Department of applied biological sciences, Faculty of Health Sciences, Université Dan Dicko Dankolodo, Maradi, Niger
⁷Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, University of Abuja, Abuja, Nigeria
⁸Department of Medicine, Faculty of Health Sciences, Université André Salifou, Niamey, Niger
⁹Department of applied biological sciences, Faculty of Health Sciences, Université Abdou Moumouni, Niamey, Niger
¹⁰Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 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


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