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 hp
Sign In
Advertise with Us
LGC Clinical Diagnostics

Download Mobile App




Pneumonia Diagnosed by Nanopore Sequencing of Sputum

By LabMedica International staff writers
Posted on 04 Oct 2018
Pathogen identification in patients with community-acquired pneumonia primarily relies on culture-based techniques. More...
Sequencing-based approaches for pathogen identification are being applied to pneumonia patients.

Haemophilus influenzae, a type of bacteria, can cause many different kinds of infections. These infections range from mild ear infections to severe diseases, like bloodstream infections. H. influenzae is an opportunistic pathogen of the respiratory tract that becomes pathogenic only when other risk factors are present.

Scientists at Seoul National University Hospital (Seoul, South Korea) and their colleagues used deep sequencing of the 16S rRNA gene from sputum to identify H. influenza in a patient with community-acquired pneumonia. They extracted genomic DNA (Genomic DNA Mini Kit from sputum obtained by oropharyngeal suction after a single empiric administration of an antimicrobial drug (cefuroxime, 500 mg). They generated the sequencing libraries using a rapid 16S amplicon sequencing kit.

The team retrospectively performed 16S amplicon sequencing with MinION, a nanopore sequencer, that is gaining attention in metagenomics studies because of its capability for long-read sequencing and real-time analysis, along with its small size. They identified the pneumonia pathogen in this patient by deep sequencing of 16S amplicons from sputum using MinION. The reads aligned to H. influenzae were >100-fold more abundant than reads aligned with other commensal bacteria, reflecting the significant proliferation of H. influenzae in the patient’s respiratory tract.

The authors concluded that with the MinION sequencer, generated reads can be analyzed in real time, which makes this approach more promising. Tentative point-of-care diagnosis by nanopore 16S sequencing and confirmation of the result by standard culture methods would be a feasible approach. They performed sequencing for five hours and the subgroup analyses of reads generated for the first hour and for the first 10 minutes produced similar results, indicating that a relatively short sequencing time would be sufficient for pathogen identification. They estimated that the turnaround time for MinION 16S sequencing can be reduced to less than eight hours. The study was published in the October 2018 issue of the journal Emerging Infectious Diseases.

Related Links:
Seoul National University Hospital


Gold Member
Troponin T QC
Troponin T Quality Control
3-Part Differential Hematology Analyzer
Swelab Alfa Plus Sampler
New
Rapid Test Reader
DIA5000
New
Automatic Hematology Analyzer
LABAS F9000
Read the full article by registering today, it's FREE! It's Free!
Register now for FREE to LabMedica.com and get access to news and events that shape the world of Clinical Laboratory Medicine.
  • Free digital version edition of LabMedica International sent by email on regular basis
  • Free print version of LabMedica International magazine (available only outside USA and Canada).
  • Free and unlimited access to back issues of LabMedica International in digital format
  • Free LabMedica International Newsletter sent every week containing the latest news
  • Free breaking news sent via email
  • Free access to Events Calendar
  • Free access to LinkXpress new product services
  • REGISTRATION IS FREE AND EASY!
Click here to Register








DIASOURCE (A Biovendor Company)

Channels

Hematology

view channel
Image: CitoCBC is the world first cartridge-based CBC to be granted CLIA Waived status by FDA (Photo courtesy of CytoChip)

Disposable Cartridge-Based Test Delivers Rapid and Accurate CBC Results

Complete Blood Count (CBC) is one of the most commonly ordered lab tests, crucial for diagnosing diseases, monitoring therapies, and conducting routine health screenings. However, more than 90% of physician... Read more

Immunology

view channel
Image: A simple blood test could replace surgical biopsies for early detecion of heart transplant rejection (Photo courtesy of Shutterstock)

Blood Test Detects Organ Rejection in Heart Transplant Patients

Following a heart transplant, patients are required to undergo surgical biopsies so that physicians can assess the possibility of organ rejection. Rejection happens when the recipient’s immune system identifies... Read more

Pathology

view channel
These images illustrate how precision oncology Organ Chips recapitulate individual patients’ responses to chemotherapy (Photo courtesy of Wyss Institute at Harvard University)

Cancer Chip Accurately Predicts Patient-Specific Chemotherapy Response

Esophageal adenocarcinoma (EAC), one of the two primary types of esophageal cancer, ranks as the sixth leading cause of cancer-related deaths worldwide and currently lacks effective targeted therapies.... Read more
Copyright © 2000-2025 Globetech Media. All rights reserved.