Genomics, MRSA and public health

Genomics is about more than humans

A lot of the time, when we talk about ‘genomics’ here at Nowgen, what we really mean is ‘human genomics’. We tend to be interested in how variations across the human genome (usually single letter changes, called ‘SNPs’ [say ‘snips’]) can alter a person’s likelihood of developing, or not developing, a particular condition.

Baby bugs

MRSA

MRSA is meticillin-resistant Staphylococcus aureus. This bacterium often hits the headlines because it is resistant to a number of widely used antibiotics, causing infections that are difficult to treat.

MRSA is more common is healthcare settings, such as hospitals or nursing homes. People can carry MRSA on their skin without being ill themselves, but often the elderly, or people in hospital are more sensitive to infections.

In 2011 a mother and baby hospital in Cambridge identified a number of newborn babies infected by MRSA. They thought there was likely to be a link between the infections – a possible outbreak, as opposed to a co-incidental occurrence of unrelated cases. As standard procedure, the hospital carried out a deep clean and reinforced their infection-control policy and practice.

Nonetheless, four days after the deep clean, another infant was identified with MRSA.

Follow the DNA code

The hospital was able to isolate the DNA from every instance of MRSA that was found. Using the DNA they could read the genetic information from each instance; something that would not have been possible just a few years ago.

Bacteria’s DNA can change really quickly and there’s plenty of opportunity for the DNA to change, because they reproduce so fast. In optimum conditions, some bacteria can reproduce every 20 minutes; in a day a single bacterium could, if unhindered, produce a colony of 4.7×1021 bacteria – more cells than you have in your entire body!

By comparing the DNA of MRSA from different individuals, the researchers worked out how each instance was related, and confirmed that it really was an outbreak. Furthermore, they were able to find out that a member of hospital staff was unwittingly spreading the infection, thus identifying the source of the outbreak. Once this member of staff was treated effectively, it stopped the spread of this outbreak.

Phylogenetic trees for an MRSA infection

Phylogenetic trees for MRSA infection

These pictures are called phylogenetic trees; they show how closely related things are – in this case, bacteria. The original instance of MRSA is in the middle; as the MRSA spread the DNA changed, and the extent of the change is reflected by how far from the middle (and how deep a shade of blue) that instance is on the tree. The left hand picture (D) shows the initial set of infections; the right hand picture (F) shows all of the instances of MRSA, including a number of different instances on the member of staff (shown with the red ‘H’), and two infections that occurred after the deep clean, through contact with that staff member.

The future

This approach to tracking an infection outbreak is new; previously, the technology did not really exist to do this. Screening the genome of MRSA means that it’s clear when there’s an outbreak and helps identify its source. In this case, the approach discovered why the outbreak continued, even after a deep clean of the affected ward(s).

Genome sequencing is not only quick, it’s also cost-effective. Each sample cost only £95 to analyse, whereas the total cost of the outbreak was estimated to cost the hospital in excess of £10,000. By identifying and treating the affected staff member, further infections were prevented, which meant that further costs were not incurred.

So, another important contribution borne out of our ability to really quickly read the genetic information contained in genomes.