https://publichealthmatters.blog.gov.uk/2014/01/20/innovations-in-genomic-sequencing/

A revolution in genomic sequencing

Microbiology is the study of microscopic organisms such as viruses and bacteria. In the past as microbiologists we would have relied on growing, staining and peering down microscopes as a way of identifying and characterising clinically important organisms, such as those that cause infections and especially human disease.

However, in the modern world, microbiologists now rely increasingly on the extraction or detection of nucleic acid, particularly for the microorganisms that we cannot culture using traditional techniques. Analysing all the complex biological data we are now able to produce often involves the creation of databases and requires computational and statistical techniques to solve the problems of managing and processing all this data. This is referred to as the field of Bioinformatics and is an integral part of modern microbiology.

Using our existing laboratory and bioinformatics methods for public health investigations has had widespread success but we have only been examining a fraction of the total (genetic) information of the pathogens we analyse. The aim of the Gastrointestinal Bacteria Reference Unit (GBRU) of Public Health England is to examine the entire genetic blueprint of a pathogen.  The GBRU has begun evaluating the use of Whole Genome Sequencing (WGS) as a fingerprinting method within the Salmonella Reference Service.

We now find ourselves at the forefront of a rapidly moving field that will ultimately impact upon the way reference laboratories deliver microbial characterization and fingerprinting. It is difficult not to feel daunted by the massive scale of this project. These changes will have a direct impact on the information available for the detection and management of infectious disease. Having said this, it is also impossible not to feel excited by the prospect of being amongst the first users of the state of the art sequencing capability at PHE.

The ‘PHE Pathogen Genomics Service’ is to be launched early in 2014 and we have already sequenced over 1500 strains of Salmonella to provide a background dataset. This is representative of about 10% of the Salmonella strains we see each year in the UK. We have already used WGS to support the management of recent outbreaks of Salmonella and it is proving to be an invaluable tool in identifying and clarifying relationships between strains and potential food sources.

The major benefit of WGS is that it provides us with an opportunity to perform strain identification and detailed fingerprinting within a single method, thus reducing the time to produce a result.  Moving forwards, we are working with our epidemiological partners to implement WGS methods into national surveillance practices and outbreak investigation.

WGS has been called the ultimate epidemiological typing method for tracing human cases to the source of the outbreak. Innovations in DNA sequencing technologies mean that we will be able deliver the total genetic information of each Salmonella strain within a time frame that will influence directly clinical and public health practice.

We do still need to do a lot more work to understand the full complexity of Salmonella and its ability to cause a variety of diseases and  although we also need to validate WGS as a fingerprinting tool, it promises to revolutionize the lives of microbiologists and bioinformaticians working in public health microbiology. How do you think these innovations will change our approach to public health in the years to come?

Leave a comment