Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia.

ABSTRACT:

Objectives

We have developed a portable system for the rapid determination of bacterial composition for the diagnosis of infectious diseases. Our system comprises of a nanopore technology-based sequencer, MinION, and two laptop computers. To examine the accuracy and time efficiency of our system, we provided a proof-of-concept for the detection of the causative bacteria of 11 meningitis patients in Zambia.

Methods

We extracted DNA from cerebrospinal fluid samples of each patient and amplified the 16S rRNA gene regions. The sequencing library was prepared, and the sequenced reads were simultaneously processed for bacterial composition determination using the minimap2 software and the representative prokaryote genomes.

Results

The sequencing results of four of the six c

SUBMITTER: Nakagawa S 

PROVIDER: S-EPMC6831930 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature