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

Principles of Disease Surveillance01:26

Principles of Disease Surveillance

228
Disease surveillance is the systematic collection, analysis, and interpretation of health data essential to the planning, implementation, and evaluation of public health practice. This process integrates data dissemination to entities responsible for preventing and controlling disease, injury, and disability. Surveillance systems provide crucial information for action, helping public health authorities make informed decisions to manage and prevent outbreaks, ensure public safety, optimize...
228
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

250
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...
250
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

14.7K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
14.7K

You might also read

Related Articles

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

Sort by
Same author

Type 3 fimbrial regulation underpins anti-MrkA immunotherapeutic efficacy in experimental Klebsiella pneumoniae infection.

The Journal of infectious diseases·2026
Same author

Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens.

PLoS biology·2026
Same author

Mortality and Length of Stay Associated With Community-Acquired Escherichia coli and Staphylococcus aureus Bloodstream Infections: An Observational Study in 9 Low- and Middle-Income Countries.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America·2026
Same author

Genetic structure of penicillin non-susceptible invasive <i>Streptococcus pneumoniae</i> in Colombia.

Microbial genomics·2026
Same author

Emergence of carbapenemase-producing Escherichia coli in acute care hospitals in 32 European countries (the CCRE survey): a prospective, multicentre, cross-sectional, epidemiological, microbiological, and genomic surveillance study.

The Lancet. Microbe·2026
Same author

Persistent spread of carbapenemase-producing Klebsiella pneumoniae in acute care hospitals in 36 European countries (the CCRE survey): a prospective, multicentre, cross-sectional, epidemiological, microbiological, and genomic surveillance study.

The Lancet. Microbe·2026

Related Experiment Video

Updated: Oct 11, 2025

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings
10:26

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Published on: August 18, 2023

5.9K

Overcoming Data Bottlenecks in Genomic Pathogen Surveillance.

Ayorinde O Afolayan1, Johan Fabian Bernal2, June M Gayeta3

  • 1Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria.

Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America
|December 1, 2021
PubMed
Summary

Whole genome sequencing (WGS) aids antimicrobial resistance surveillance by identifying resistance trends, evolutionary mechanisms, and transmission routes. Addressing informatics and bioinformatics bottlenecks enables broader WGS implementation globally.

Keywords:
WGSantimicrobial resistancebioinformaticsmetadatawhole genome sequencing

More Related Videos

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.5K
Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
09:44

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Published on: December 23, 2022

2.5K

Related Experiment Videos

Last Updated: Oct 11, 2025

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings
10:26

Author Spotlight: A Cost-Effective Genomic Workflow for Advancing Rabies Control in Resource-Limited Settings

Published on: August 18, 2023

5.9K
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

2.5K
Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
09:44

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing

Published on: December 23, 2022

2.5K

Area of Science:

  • Genomics
  • Microbiology
  • Epidemiology

Background:

  • Whole genome sequencing (WGS) is crucial for tracking antimicrobial resistance (AMR) at various scales.
  • Implementing WGS involves complex informatics and bioinformatics procedures that can be challenging for laboratories.

Purpose of the Study:

  • To describe data bottlenecks in WGS for AMR surveillance.
  • To present solutions implemented in laboratories in India, Colombia, Nigeria, and the Philippines.
  • To facilitate wider adoption of WGS for AMR surveillance.

Main Methods:

  • Utilized reproducible data parsing pipelines and genome sequence analysis workflows.
  • Employed technologies such as Data-flo, Nextflow workflow manager, and containerization.
  • Focused on overcoming informatics and bioinformatics barriers.

Main Results:

  • Successfully addressed data bottlenecks in WGS implementation for AMR surveillance.
  • Enabled WGS adoption in diverse international laboratory settings.
  • Facilitated the building of evidence for AMR surveillance.

Conclusions:

  • Overcoming WGS data challenges is key to enhancing global AMR surveillance.
  • Standardized workflows and tools improve the feasibility of pathogen genomics.
  • WGS implementation supports the discovery of resistance mechanisms and transmission dynamics.