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.
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.
Microbial whole-genome sequencing is the primary NGS method for molecular epidemiology.
Featured Molecular Epidemiology Articles
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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Molecular Epidemiology of Foodborne and Animal Pathogens
Illumina NGS helps this lab efficiently detect and track animal and food pathogens.
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Illumina Sequencers Help Characterize and Control Coronavirus
This detailed viral information is enabling public health officials to respond with unprecedented speed and breadth.
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How Sequencing-Based Surveillance Helps Fight COVID-19
Q&A with Chief Medical Officer Phil Febbo, MD
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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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Illumina and IDbyDNA Partner to Deliver NGS Infectious Disease Solutions
Partnership aims to accelerate NGS adoption for clinical infectious disease testing
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Additional Resources
NGS in Veterinary Epidemiology
Tony Goldberg and Sam Sibley discuss how NGS is driving progress in infectious disease epidemiology for veterinary medicine.
Tracking Influenza Using NGS
Learn about the culture-free method developed at AFRIMS in Thailand for tracking influenza using MiSeq.
H7N9 Influenza Surveillance in China
Read how dedicated researchers at the Jiangsu CDC use MiSeq for H7N9 influenza surveillance.
Epidemiology of Drug-Resistant Bacteria
Researchers use NGS to understand the evolution and spread of methicillin-resistant Staphylococcus aureus.
References
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.