May 23rd, 2013 12:26 pm ET - Marta Gwinn, Consultant, McKing Consulting Corp, Office of Public Health Genomics, Centers for Disease Control and Prevention
The proposed Advanced Molecular Detection initiative aims to help CDC apply molecular sequencing and bioinformatics techniques to solving outbreaks and controlling infectious diseases. This approach has been called “genomic epidemiology”—using pathogen genome sequences to detect emerging diseases, assess their potential virulence and resistance to antibiotics, and monitor their spread in populations. The focus is on pathogen genomes, applying advances in molecular and bioinformatics methods first developed for human genome research.*
Each week, OPHG’s Genomics & Health Impact Update includes a list of articles on genomics published by CDC scientists. These articles are selected from the latest edition of Science Clips, an online bibliographic digest that CDC shares weekly with the public health community and the public. What genomic studies are CDC public health scientists doing—and which genomes are they writing about? We went to the archives to find out.
In 2012, Science Clips listed 178 articles on genomics with one or more CDC authors. Of these, 111 (62%) concerned bacterial, viral, fungal, or parasite genomes; 61 (34%) concerned the human genome; and 6 (3%) concerned genomes of other animal species (Figure).
Most of the 61 articles on human genomics were related to epidemiology. Nearly half were epidemiologic studies; others described or applied epidemiologic methods (Table).
Table. CDC-authored articles on human genomics, 2012.
|n||(%)||Type of study|
|28||(46)||Epidemiologic studies of genotype prevalence, gene-disease association, and gene-environment interaction|
|6||(10)||Other types of primary data collection (3 surveys; 1 each clinical trial, screening, in vitro)|
|6||(10)||Reviews or recommendations|
|2||(3)||Epidemiologic or statistical methods development|
Of the 111 articles that described research on microbial genomes (bacterial, viral, fungal, or parasite), approximately half (n=58) reported their source as human surveillance or clinical samples; 3 of these articles also described samples obtained from animals or animal products. Of the 58 human-derived samples, 26 (45%) were collected through surveillance or epidemiologic surveys and 10 (17%) were from outbreaks. The remaining 53 articles described samples obtained from other (non-human) sources, of which 14 (26%) described one or more animal sources, including insects, arthropods, mollusks, birds, and mammals.
Genomes are found at all three corners of the epidemiologic triangle: human or animal hosts are engaged in genomic contests with pathogens of all kinds, played out in an environment teeming with the genomes of other people, animals, plants, and microbes.
Until recently, only the simplest genomes were available to public health scientists and even those were generally known only by their fingerprints. Now, genomic sequencing technology has brought the world in reach: whole genome sequences of pathogens, to study their biology and epidemiology; animals, plants, and environmental microbes, to study their evolution and ecology through meta-genomics and microbiome analysis; and humans, to study their susceptibility, resilience, potential to transmit infection, and response to interventions. It’s a genomic world.