Abstract
Epidemiologists aim to inform the design of public health interventions with evidence on the evolution, emergence and spread of infectious diseases. Sequencing of pathogen genomes, together with date, location, clinical manifestation and other relevant data about sample origins, can contribute to describing nearly every aspect of transmission dynamics, including local transmission and global spread. The analyses of these data have implications for all levels of clinical and public health practice, from institutional infection control to policies for surveillance, prevention and treatment. This review highlights the range of epidemiological questions that can be addressed from the combination of genome sequence and traditional ‘line lists’ (tables of epidemiological data where each line includes demographic and clinical features of infected individuals). We identify opportunities for these data to inform interventions that reduce disease incidence and prevalence. By considering current limitations of, and challenges to, interpreting these data, we aim to outline a research agenda to accelerate the genomics-driven transformation in public health microbiology.
Highlights
Infectious disease epidemiologists study patterns of disease incidence, and seek ways to turn observations about which individuals and populations become infected into strategies to decrease the burden of disease
Studies of influenza A/H3N2 show that China and South-east Asia are frequently the source of the lineages that circulate globally [8,9,10]. What does this new level of detail offer to the infectious disease epidemiologist? Whereas the sequence of a single organism or clone can address questions about the microbe’s phenotype and history [11,12], comparisons of larger numbers of genome sequences can shed light on evolution and population genetics, using little other than the date of isolation in combination with sequence [13,14,15,16]
The combination of genome sequence data from clinical and environmental isolates and epidemiological data about the sources of the isolates can help characterize the origins, transmission, dynamics and evolution of infectious disease epidemics, with examples ranging from understanding how the pneumococcal population has evolved in response to use of antipneumococcal vaccination in children [14] to the sources and spread of the ongoing Ebola epidemic in West Africa [17]
Summary
Infectious disease epidemiologists study patterns of disease incidence, and seek ways to turn observations about which individuals and populations become infected into strategies to decrease the burden of disease. What does this new level of detail offer to the infectious disease epidemiologist? The combination of genome sequence data from clinical and environmental isolates and epidemiological data about the sources of the isolates can help characterize the origins, transmission, dynamics and evolution of infectious disease epidemics, with examples ranging from understanding how the pneumococcal population has evolved in response to use of antipneumococcal vaccination in children [14] to the sources and spread of the ongoing Ebola epidemic in West Africa [17]. We discuss the importance of these tools by
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