Genomic technologies in infectious diseases
Genomics and next generation sequencing has already lead to a revolution in infectious diseases and promises to continue this trend as the technologies improve, get cheaper and become a ubiquitous and indispensable tool.
Infectious diseases occur as a result of the interaction between host and microorganism and involve multiple genomes. The information gained from accessing the genomes of both host and pathogen already plays an important role in developing the understanding of microorganisms (in health and disease), including identification of novel species, understanding more about how and why the infection occurred, and aiding the development of new drug and vaccine targets. The utility of next generation sequencing is not limited to a research setting and in a clinical setting it is emerging as a useful tool in diagnostics, guiding therapy and providing epidemiological information for infection control and public health teams.
With previously available technologies, it was not possible to culture all microorganisms in an agnostic manner, i.e. without knowing what you were looking for. Next generation sequencing does not require any prior knowledge, and can provide information about all pathogens directly from clinical samples.
With a number of genomes to choose from, next generation sequencing offers a number of current and potential applications:
Whole genome sequencing of the pathogen – providing a wealth of information including virulence factors, drug resistance and epidemiological typing data.
Whole genome sequencing of the host - providing useful information regarding genetic susceptibility to infectious diseases.
Microbiome analysis – targeting a particular gene (often the bacterial ribosomal 16S RNA) to investigate the bacterial community at a particular site.
Metagenomics - sequencing en masse nucleic acids extracted from complex microbial communities providing information where the unit of study is at the level of the bacterial community.
The Paradigm of Tuberculosis
The potential benefit of sequencing the whole genome of a single organism is perhaps usefully illustrated by considering Mycobacterium tuberculosis. Tuberculosis is an important burden on healthcare requiring not only a prolonged course of medication for the patient but also public health intervention to manage and minimise potential spread of infection. Timely diagnosis and identification of drug resistance is the key to successfully managing this infection. M.tuberculosis is slow growing, sometimes requiring weeks to grow. Even once a pure culture of the organism is obtained it then can take many weeks before treatment sensitivities are available. Having access to the full genomic information from an individual patient not only enables the search for mutations associated with resistance to multiple drugs but also has the potential to significantly reduce the time taken to identify drug resistance allowing earlier treatment modification. Additionally, typing organisms using the whole genome offers the chance not only to identify closely related strains but to track transmission of infection at a finer level of detail.
Microbiomes in Health and Disease
Humans are host to myriad microorganisms in various ecological niches within the body. There is an increasing appreciation that these commensal organisms are important not only in health but also disease (both infectious and non-infectious). Profiling of these bacterial communities can be undertaken by sequencing a particular gene that is present in the different members of the community. The bacterial 16S ribosomal RNA gene is often used as it is highly conserved amongst species of bacteria and archaea. It has conserved regions flanking variable regions allowing for the design of primers that allow sequencing of portions of the gene and subsequent identification of the different bacterial species in the sample. Investigating how the structure of the bacterial population develops and changes in different settings may not only provide useful information regarding pathogenesis but also offers the potential for earlier diagnosis and intervention.
Next generation sequencing has already fundamentally changed the world of infectious diseases and holds much promise for continuing this revolution. It is already emerging as a useful diagnostic tool to be used in conjunction with more traditional methods. The challenge that we will likely face is not going to be a lack of genomic information but deciding what is clinically relevant and what it all means.
© Paul Randell, St George’s University of London