Sanger Institute - Tracking MRSA Outbreak

MRSA stands for methicillin-resistant Staphylococcus aureus
Staphylococcus aureus is a bacterium that lives on normal healthy people
But the difference with MRSA is that it is acquired resistance to an antibiotic called methicillin
MRSA is an important healthcare problem because patients who come into hospital occasionally get infected with this organism
And if they do so then that increases the length of their hospital stay
It can increase cost of healthcare and obviously causes harm to the individual patient
People in high intensity settings such as intensive care units are swabbed every week
to see if they've acquired MRSA carriage
If we find two or more people who have then we suspect an outbreak has occurred
Under those circumstances the infection control team will go and investigate
To see whether they can form links in time between two individuals
It's a challenge to identify an outbreak because most MRSAs from UK hospitals are from
A very, very tightly related group of organisms, a clone if you'd like
And MRSA from various hospitals from across the UK and in fact across the world will look identical
By current typing techniques, so therefore you can't tell if you've caught your MRSA from
The person next to you or from a visitor or if you brought it into hospital with you
In order to be able to tell two bacteria apart, two MRSA strains apart
One would need a much more discriminatory typing technique than what we have at the moment
What we've shown in this work is that newer technologies, which perform the same sequencing
process, the whole genome sequencing process, but at much, much greater speed
Can generate the data that we need in a timescale that is relevant to identifying outbreaks
Our aim was to apply whole genome sequencing to an outbreak investigation on a neonatal intensive care unit
To see whether we could group isolates that were associated with the outbreak
And exclude those that were not. We generated this information in just one day
The experiment we actually did was retrospective, we knew the outbreak had already occurred
But we took these techniques and applied them as if the outbreak was going on in real time
And we found firstly what we expected to find which was, the strains that we thought were part of the outbreak
Could be shown to be part of an outbreak by this technology but in a much more rapid timescale
But what we also found that was unexpected is that we sequenced a number of controlled strains
other MRSA strains that were around in the hospital at the same time
And we identified a transmission event that had previously been missed
Purely by seeing these strains were identical at the genome level
Whole genome sequencing also allowed us to see all of the genes in the bacterial genome
This allows us to detect antibiotic resistance genes, genes that encode for virulence factors such as toxins
And knowing this could help us change the way we treat patients in the future
We think that if this technique were in routine use, which we hope it will be in a few years
Then we will be able to identify potential outbreaks much earlier
And intervene in those outbreaks much earlier
And therefore prevent a lot of down-stream problems that currently accrue from outbreaks occurring in hospitals
The next steps are to develop interpretation tools that interpret whole genome sequence
Into an output that can be understood by healthcare workers with no specialist knowledge in genomics
The beauty of this technology is that it could be applied to a range of other pathogens
That cause both in hospitals and in communities
That could allow us to track transmission more accurately
And the benefit that would bring is that we could detect outbreaks more quickly
And intervene more rapidly to bring the outbreak to a close