We use cookies to understand how you use our site and to improve your experience. This includes personalizing content and advertising. To learn more, click here. By continuing to use our site, you accept our use of cookies. Cookie Policy.

Features Partner Sites Information LinkXpress
Sign In
Advertise with Us
Abbott Diagnostics- Hematology Division


Illumina develops, manufactures and markets integrated systems for the analysis of genetic variations and biological ... read more Featured Products: More products

Download Mobile App


ATTENTION: Due to the COVID-19 PANDEMIC, many events are being rescheduled for a later date, converted into virtual venues, or altogether cancelled. Please check with the event organizer or website prior to planning for any forthcoming event.
23 Sep 2021 - 25 Sep 2021

Molecular Characterization of Microbiota in Cerebrospinal Fluid Using WGA

By LabMedica International staff writers
Posted on 02 Sep 2021
Print article
Image: The MiSeq benchtop sequencer enables targeted and microbial genome applications, with high-quality sequencing, simple data analysis, and cloud storage (Photo courtesy of Illumina)
Image: The MiSeq benchtop sequencer enables targeted and microbial genome applications, with high-quality sequencing, simple data analysis, and cloud storage (Photo courtesy of Illumina)
Hydrocephalus is a common cause of neurological disability in children. Cerebrospinal fluid (CSF) shunt placement allows children with hydrocephalus to survive and avoid ongoing brain injury.

Understanding the etiology of cerebrospinal fluid shunt infections and reinfections requires detailed characterization of associated microorganisms. Traditionally, identification of bacteria present in the CSF has relied on culture methods, but recent studies have used high throughput sequencing of 16S rRNA genes.

Neurosurgeons at the Seattle Children’s Hospital (Seattle, WA, USA) and their colleagues enrolled in a study a subset of children who failed treatment for CSF shunt infection (i.e. had CSF shunt reinfection) and had CSF collected both near the beginning and end of both infection episodes. All samples were tested by routine CSF aerobic culture in hospital-certified laboratories.

DNA was extracted and purified from CSF samples using the AGOWA mag Mini DNA isolation kit (AGOWA, LGC Genomics, Berlin, Germany) and CSF microbiota amplicon library construction was carried out using a one-step PCR amplification targeting the V4 region of the bacterial 16S rRNA gene. Sequencing of the pooled libraries was carried out for 600 cycles on an Illumina MiSeq desktop sequencer using the MiSeq Reagent Kit v3 (Illumina, San Diego, USA). Whole genome amplification (WGA) of DNA purified from CSF samples and two mock community samples was carried out using the REPLI-g Mini Kit (Qiagen, Hilden, Germany) and sequenced on the Illumina HiSeq 2500 platform to produce 96-bp paired-end reads.

Taxonomic assignments of sequences from WGA and 16S were compared with one another and with conventional microbiological cultures. While classification of bacteria was consistent among all the approaches, WGA provided additional insights into sample microbiological composition, such as showing relative abundances of microbial versus human DNA, identifying samples of questionable quality, and detecting significant viral load in some samples. One sample yielded sufficient non-human reads to allow assembly of a high-quality Staphylococcus epidermidis genome, denoted CLIMB1, which we characterized in terms of its multilocus sequence typing (MLST) profile, gene complement (including putative antimicrobial resistance genes), and similarity to other annotated S. epidermidis genomes.

The authors concluded that they had demonstrated that WGA directly applied to CSF is a valuable tool for the identification and genomic characterization of dominant microorganisms in CSF shunt infections, which can facilitate molecular approaches for the development of better diagnostic and treatment methods. The study was published on August 20 2021 in the journal Frontiers in Cellular and Infection Microbiology.

Related Links:
Seattle Children’s Hospital
LGC Genomics

Gold Supplier
Digital Trichoscope
Silver Supplier
Lipid Profile Analyzer
Cholestech LDX
Urea Breath Test System for H. Pylori
BreathID Hp Lab
Single Channel Pipette
AHN pipet4u pro

Print article



view channel
Image: The CellSearch Circulating Tumor Cell Kit is intended for the enumeration of circulating tumor cells of epithelial origin (CD45-, EpCAM+, and cytokeratins 8, 18+, and/or 19+ and PD-L1) in whole blood (Photo courtesy of CellSearch/Menarini Silicon Biosystems)

PD-L1 Expression in Circulating Tumor Cells Investigated for NSCLC

In non-small cell lung cancer (NSCLC), analysis of programmed cell death ligand 1 (PD-L1) expression in circulating tumor cells (CTCs) is a potential alternative to overcome the problems linked to the... Read more


view channel

Global Digital Polymerase Chain Reaction (dPCR) Market Projected to Reach Close to USD 1.15 Billion by 2028

The global digital polymerase chain reaction (dPCR) market is projected to grow at a CAGR of more than 9% from over USD 0.50 billion in 2020 to nearly USD 1.15 billion by 2028, driven primarily by rising... Read more
Copyright © 2000-2021 Globetech Media. All rights reserved.