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Genomic analysis could help win the fight against superbugs

Whole genome sequencing can help identify the source of the antibiotic resistance. Shutterstock

Some recent headlines from Australian newspapers: NSW hospitals worst place for Golden Staph; CA-MRSA - the killer in our midst; Superbug onslaught.

By now, most people are aware that antibiotic-resistant bacteria are a serious problem, as the above headlines demonstrate. The government is aware of the issue as well.

Two reports in the past month — one from the Office of the Chief Scientist and the other from the Antimicrobial Resistance Standing Committee – have called for action on antibiotic resistance in Australia.

Both recognised that we need co-ordinated, nationwide surveillance of antibiotic-resistant infections to avoid the nightmare of untreatable infections in hospitals.

A good place to start would be to invest in DNA-sequencing technology, supercomputers, and training more people in bioinformatics, a discipline that uses computers to extract meaningful information from genomic data.

Why? Because if we want to monitor where resistance comes from and how it spreads, genome analysis technology is a big part of the answer. Here’s an example of how it works.

Genomics in action

Vancomycin-resistant Enterococcus faecium (VRE) is overtaking golden Staph as the leading cause of antibiotic-resistant bloodstream infections in some Australian hospitals.

Until recently, it was assumed that clusters of VRE cases in hospitals were caused by resistant bacteria spreading from one patient to another, so hospitals have been trying to stop the spread of the bug by isolating infected patients at great expense.

A recent study at the Austin Hospital in Melbourne employed whole genome sequencing to investigate, in the finest forensic detail possible, the relationship between VRE from different patients. The results were a surprise - the bacteria differed substantially, too much to be the result of spreading within the hospital.

Instead, the study suggests that some patients who develop VRE infections in hospital probably had the bacteria, or a precursor, inside them when they arrived there, as opposed to picking up bugs from other patients.

So, isolating infected patients may not always help. Rather, we could prevent VRE infections by checking new patients to see if they are carrying the bug in their gut. And if they have VRE, and go on to develop an infection in hospital, doctors will know not to waste time with the wrong antibiotics.

Of course, hand hygiene and clean hospitals remain critical for stopping the spread of infections between patients.

Resistance can develop during antibiotic treatment

Every time a bacterium meets a drug, there is a risk that it will develop resistance. When antibiotics are used unnecessarily - to treat viral infections or bacterial infections where they have a minimal effect - they increase the risk of drug-resistant bacteria emerging.

For example, if you take antibiotics for a cough that’s caused by a viral respiratory infection, it won’t make you better, but it could prompt your friendly gut bacteria to develop antibiotic resistance. You probably won’t notice this because those bugs are living happily in your stomach and doing you no harm.

But if you then have an accident, or become sick and require surgery, those bugs could get into your bloodstream and cause serious systemic infections, or septicaemia, that is very hard to treat.

So, careful and controlled use of antibiotics, or “antibiotic stewardship”, is important to prevent new resistant bugs from developing.

Once a bacterium becomes resistant, it can spread to other people and cause more resistant infections. This is a serious problem in hospitals, where resistance develops in a patient receiving antibiotics, creating a superbug that can spread to other patients.

Worse, bacteria can also share their resistance by transferring bits of DNA between cells. So when one bug learns a new trick, it can quickly teach others. We need to understand this much better so that we can prevent or manage it. But the only way we can detect this happening is through DNA surveillance of bacteria.

This is why DNA sequencing of bacteria has become the new gold standard for tracking the emergence and spread of resistance.

Critical questions that genomics can help answer

Genomics can help us identify the source of the infection and how the resistance develops.

Much like forensics can link a suspect to a crime, DNA tracking can link a suspected source (say, a dirty sink) to a patient’s infection. This allows us to monitor the spread of resistant bacteria between hospitals and between states, as well as the introduction of new resistant bugs from overseas.

This information can be important for deciding when to isolate patients or introduce quarantine measures.

We also need to know how often resistance develops during treatment, and how often resistance spreads between patients.

If the problem is mainly one of spread, we need to concentrate on hand hygiene, isolating affected patients and other methods, to try to limit spread in hospitals. But if most resistance arises during treatment, we need to change our antibiotic prescribing habits to avoid this.

These questions are best addressed by whole genome sequencing. The technology is available, and we have the expertise in Australia to implement it for surveillance and infection control.

All it needs is an investment of resources. And as both recent reports have pointed out - like many reports over the past 15 years - action is needed now.

Kathryn Holt is the winner of a 2013 L'Oréal For Women in Science Fellowship.

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