Examine variations across host and pathogen genomes

Better understand the mechanisms that lead to infection and spread

Molecular Epidemiology

Molecular epidemiology describes a process of identifying the genetic basis of disease, including variants within hosts and pathogens that influence infection, transmission, and prevention. Molecular epidemiologists typically focus on determining sources of infection, tracking transmission routes, and identifying genes responsible for virulence and drug resistance, to support hospital infection control and epidemiological investigations.

Next-generation sequencing (NGS) allows highly accurate, hypothesis-free analysis of multiple isolates for detection, replacing multiple tests to identify organisms and examine resistance and virulence. In contrast, traditional methods of pathogen identification and characterization are often guided by serial hypotheses and are optimized for only a limited number of organisms.

Human Microbiome Analysis

Featured Molecular Epidemiology Articles

iSeq used to study Ebola outbreak
Characterizing an Ebola Outbreak

In combination with extensive epidemiological findings, the portable iSeq 100 System enabled local scientists to analyze transmission patterns and trace the outbreak's origin.

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Pseudomonas Aeruginosa
Surveillance of Infections with Bacterial Genome Sequencing

Healthcare-acquired infections are a major healthcare concern. Outbreak detection is possible through comprehensive isolate discrimination and characterization.

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Illumina Sequencers Help Characterize and Control Coronavirus

Illumina NGS was used to sequence the SARS-CoV-2 coronavirus genome, in combination with other technologies, as published in the New England Journal of Medicine.

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COVID-19 Sequencing

Compare NGS methods and find solutions to detect and characterize SARS-CoV-2, track transmission routes, study co-infection, and investigate viral evolution. 

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COVID-19 Solutions

A key advantage of NGS is that researchers can generate genome sequence data capable of identifying a range of organisms (bacteria, viruses, and parasites). Examining variations across genomes supports cross-sectional studies for better understanding of mechanisms that lead to infection and spread, as well as phylogenetic analysis to determine relatedness among organisms. 

High-resolution pathogen typing using whole-genome sequencing data can differentiate organisms that many older methods cannot distinguish.

Microbial whole-genome sequencing can help epidemiologists overcome traditional challenges of tracking disease origins and investigating outbreaks.

Tracking Pathogenic Changes

Get an introduction to genomic epidemiology as Dr. Jennifer Gardy explains how NGS is adding muscle to public health efforts and how it was used to reconstruct outbreaks of tuberculosis in British Columbia, Canada.

Read article: Staying Ahead of the Next Outbreak

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Infectious Disease Surveillance

NGS supports effective strategies to identify emerging pathogens, study zoonotic reservoirs, and prevent further transmission.

Respiratory Pathogen ID/AMR Panel

This NGS-based workflow targets respiratory pathogens and antimicrobial resistance alleles, and offers simplified data analysis powered by IDbyDNA.

COVID-19 Software Tools

Accelerate coronavirus detection and identification, perform host response studies, simplify your sample tracking, and contribute to public databases, free of charge.

Podcast stories explore unusual and surprising applications of genomics
Podcast stories explore unusual and surprising applications of genomics

Illumina partners with Naked Genetics to engage audiences in the world of next-generation sequencing

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The Time is Now for Microbiome Studies
The Time is Now for Microbiome Studies

Whole-genome shotgun sequencing and transcriptomics provide researchers and pharmaceutical companies with data to refine drug discovery and development.

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Reaching new heights in data quality and throughput on a benchtop sequencer
Reaching new heights in data quality and throughput on a benchtop sequencer

At AGBT 2024, Illumina presented several studies, highlighting improvements to NextSeq Systems and more

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NGS in Veterinary Epidemiology

Tony Goldberg and Sam Sibley discuss how NGS is driving progress in infectious disease epidemiology for veterinary medicine.

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Tracking Influenza Using NGS

Learn about the culture-free method developed at AFRIMS in Thailand for tracking influenza using MiSeq.

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H7N9 Influenza Surveillance in China

Read how dedicated researchers at the Jiangsu CDC use MiSeq for H7N9 influenza surveillance.

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NGS for Microbial Genomes and Infection Control
Epidemiology of Drug-Resistant Bacteria

Researchers use NGS to understand the evolution and spread of methicillin-resistant Staphylococcus aureus.

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  1. Prosperi M, Veras N, Azarian T, Rathore M, Nolan D, et al. (2013) Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the genomic era: a cross-sectional study. Sci Rep 3: 1902.
  2. FBurnham CA, Carroll KC (2013) Diagnosis of Clostridium difficile infection: an ongoing conundrum for clinicians and for clinical laboratories. Clin Microbiol Rev 26:604–30.
  3. Crawford DC, Goodloe R, Brown-Gentry K, Wilson S, Roberson J, et al. (2013) Characterization of the Metabochip in diverse populations from the International HapMap Project in the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) project. Pac Symp Biocomput 188–199.
  4. Harrison EM, Paterson GK, Holden MT, Larsen J, Stegger M, et al. (2013) Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC. EMBO Mol Med 5:509–15.
  5. Smura T, Kakkola L, Blomqvist S, Klemola P, Parsons A, et al. (2013) Molecular evolution and epidemiology of echovirus 6 in Finland. Infect Genet Evol 16C:234–247.
  6. Pérez-Losada M, Cabezas P, Catro-Nallar E., Crandall KA. (2013) Pathogen typing in the genomics era: MLST and the future of Molecular Epidemiology. Infect Genet Evol 16C:38–53.