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Microbial Genomics

Examine variations across host and pathogen genomes

Better understand the mechanisms that lead to infection and spread

Molecular Epidemiology

Introduction to 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. Researchers determine the sources of infection, route of transmission, and molecular pathways and genes responsible for virulence and drug resistance to support hospital infection control and epidemiological investigations.

Traditional methods of pathogen identification and characterization are often are guided by serial hypotheses and are optimized for a only limited number of organisms.

Human Microbiome Analysis

Next-Generation Sequencing for Molecular Epidemiology

Next-generation sequencing (NGS) allows highly accurate, hypothesis-free analysis of multiple isolates for detection, replacing multiple tests to identify the organism and examine resistance and virulence. High-resolution pathogen typing using whole-genome sequencing data can differentiate organisms that many current methods cannot distinguish.

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.

The primary NGS application for molecular epidemiology is whole-genome sequencing.

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Additional Resources

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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
NGS for Microbial Genomes and Infection Control

Global collaboration of researchers is using the MiSeq System to understand the evolution and spread of drug-resistant bacteria.

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Metagenomics for Virus Discovery on Skin
Metagenomics for Virus Discovery on Skin

Illumina sequencers offer deep coverage to identify novel HPV types correlated with non-melanoma skin cancers.

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Tracking Foodborne Pathogens with NGS
Tracking Foodborne Pathogens with NGS

MiSeq System helps this lab perform agri-food pathogen testing and epidemiology efficiently.

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References
  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.