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 (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.