Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

574
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
574
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

500
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
500
Methods of Classification and Identification01:28

Methods of Classification and Identification

976
Bacterial identification relies on a diverse array of techniques to classify and understand microorganisms, each tailored to uncover specific characteristics. Traditional morphological approaches, while still valuable, are limited for closely related or structurally simple organisms. Modern methods integrate biochemical, serological, genetic, and advanced molecular tools to achieve greater accuracy.Morphological and Biochemical TechniquesMorphological characteristics, such as cell shape and...
976

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A Single Amino Acid Substitution in CspA Increases Germination Sensitivity and Broadens Bile Salt Germinant Specificity in Clostridioides difficile Spores.

Environmental microbiology·2026
Same author

Interregional outbreak of <i>Salmonella Typhimurium</i> linked to fresh cheese: A case-case study guided by whole-genome sequencing (WGS), Portugal, March-June 2024.

Epidemiology and infection·2026
Same author

Genome Sequencing in Infectious Disease Outbreaks.

Advances in experimental medicine and biology·2026
Same author

Vibrational spectroscopy as a complementary approach to monitor SH-SY5Y cell differentiation.

Analytical biochemistry·2026
Same author

Decoding azole resistance mechanisms and pathogenicity in Aspergillus section Fumigati through genomic analysis.

Fungal genetics and biology : FG & B·2026
Same author

One-Month Rifapentine-Isoniazid Regimen Versus Six-Month Isoniazid Monotherapy for Latent Tuberculosis: Experience from a Reference Center.

Medicina (Kaunas, Lithuania)·2026

Related Experiment Video

Updated: Jan 12, 2026

High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR
11:00

High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR

Published on: November 28, 2016

12.3K

Probe-based metagenomic pathogen detection: advancing laboratory capacity for complex diagnosis.

Rita Ferreira1, Luís Coelho1, João Dourado Santos1

  • 1Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.

Frontiers in Microbiology
|October 30, 2025
PubMed
Summary

This study evaluated probe-based pathogen detection panels for complex diagnoses. The INSaFLU-TELEVIR(+) pipeline improved pathogen detection rates, especially for bacteria and viruses, aiding clinical decision-making.

Keywords:
INSaFLU-TELEVIRbioinformatics analysismNGSmetagenomicsnext-generation sequencingpathogen detection

More Related Videos

Author Spotlight: Advancing Rapid Detection of Respiratory Pathogens Using Microfluidic Chip
06:11

Author Spotlight: Advancing Rapid Detection of Respiratory Pathogens Using Microfluidic Chip

Published on: March 29, 2024

2.3K
Amplicon Sequencing using the Long-Read Sequencing Technologies
08:57

Amplicon Sequencing using the Long-Read Sequencing Technologies

Published on: August 29, 2025

474

Related Experiment Videos

Last Updated: Jan 12, 2026

High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR
11:00

High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR

Published on: November 28, 2016

12.3K
Author Spotlight: Advancing Rapid Detection of Respiratory Pathogens Using Microfluidic Chip
06:11

Author Spotlight: Advancing Rapid Detection of Respiratory Pathogens Using Microfluidic Chip

Published on: March 29, 2024

2.3K
Amplicon Sequencing using the Long-Read Sequencing Technologies
08:57

Amplicon Sequencing using the Long-Read Sequencing Technologies

Published on: August 29, 2025

474

Area of Science:

  • Clinical Microbiology
  • Next-Generation Sequencing (NGS)
  • Bioinformatics

Background:

  • Shotgun metagenomics faces challenges with low microbial DNA ratios and high computational demands.
  • Probe-based pathogen enrichment coupled with NGS offers a promising alternative for complex diagnostics.
  • The Respiratory and Urinary Pathogen ID panels (RPIP and UPIP) are designed for pathogen detection.

Purpose of the Study:

  • To assess the combined detection performance of RPIP and UPIP using diverse clinical samples.
  • To compare the performance of Illumina's Explify solution with an extended metagenomics pipeline (INSaFLU-TELEVIR(+)).
  • To validate a novel diagnostic approach for complex infectious disease cases.

Main Methods:

  • Utilized 99 clinical samples across 15 different matrices from Portuguese National Reference Laboratories.
  • Employed two Illumina probe-based panels (RPIP and UPIP) for pathogen enrichment.
  • Analyzed data using Illumina's Explify solution and an extended INSaFLU-TELEVIR(+) metagenomics pipeline with taxonomic classification and read mapping.

Main Results:

  • The INSaFLU-TELEVIR(+) pipeline achieved an overall detection rate of 79.8% (91/114) of PCR-positive targets, improving upon Explify's 73.7% (84/114).
  • Detection rates increased for bacteria (54.3% to 65.7%) and viruses (85.3% to 89.7%) with the extended pipeline.
  • The workflow demonstrated high efficacy for samples with high qPCR Ct values (≥30), detecting 71.8% of targets.

Conclusions:

  • The combined use of probe-based panels and the INSaFLU-TELEVIR(+) pipeline enhances pathogen detection in complex clinical samples.
  • This validated approach represents a significant advancement for the Portuguese National Institute of Health in supporting clinicians.
  • The improved diagnostic capabilities can lead to more informed clinical decisions and better infectious disease management outcomes.