Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting

Srinivas Reddy Pallerla, Do Van Dong, Le Thi Kieu Linh, Trinh Van Son, Dao Thanh Quyen, Phan Quoc Hoan, Ngo Tat Trung, Nguyen Trong The, Jule Rüter, Sébastien Boutin, Dennis Nurjadi, Bui Tien Sy, Peter G Kremsner, Christian G Meyer, Le Huu Song, Thirumalaisamy P Velavan

Abstract

AIM: The aim of the present study is to compare the performance of 16S rRNA Nanopore sequencing and conventional culture in detecting infectious pathogens in patients with suspected meningitis in a resource-limited setting without extensive bioinformatics expertise.

METHODS: DNA was isolated from the cerebrospinal fluid (CSF) of 30 patients with suspected bacterial meningitis. The isolated DNA was subjected to 16S sequencing using MinION™. The data were analysed in real time via the EPI2ME cloud platform. The Nanopore sequencing was done in parallel to routine microbiological diagnostics.

RESULTS: Nanopore sequencing detected bacterial pathogens to species level in 13 of 30 (43%) samples. CSF culture showed 40% (12/30) positivity. In 21 of 30 patients (70%) with suspected bacterial meningitis, both methods yielded concordant results. About nine of 30 samples showed discordant results, of these five were false positive and four were false negative. In five of the culture negative results, nanopore sequencing was able to detect pathogen genome, due to the higher sensitivity of the molecular diagnostics. In two other samples, the CSF culture revealed Cryptococcus neoformans and Streptococcus pneumoniae, which were not detected by Nanopore sequencing. Overall, using both the cultures and 16S Nanopore sequencing, positivity rate increased from 40% (12/30) to 57% (17/30).

CONCLUSION: Next-generation sequencing could detect pathogens within six hours and could become an important tool for both pathogen screening and surveillance in low- and middle-income countries (LMICs) that do not have direct access to extensive bioinformatics expertise.

Original languageEnglish
JournalAnnals of Clinical Microbiology and Antimicrobials
Volume21
Issue number1
Pages (from-to)39
ISSN1476-0711
DOIs
Publication statusPublished - 05.09.2022

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