Genome researchers track and stop spread of killer bug

An outbreak of a drug-resistant bacterial bug, which killed six people and infected 11 more, was stopped partially
thanks to genome sequencing, a paper in Science Translational Medicine reports.

The outbreak was triggered after a 43-year-old woman was
admitted to the intensive care unit at the National Institutes of Health (NIH) research hospital in
Maryland, USA. She had been diagnosed with an infection of the bacterium Klebsiella pneumoniae and was immediately put into
quarantine.

K. pneumoniae kills around half of all people diagnosed with
it, and resists most antibiotics. It can also be spread by carriers who show no
symptoms of infection.

The hospital
used a technique known as 'enhanced contact isolation', enforcing the use of
masks and gloves at all times, disinfecting all equipment and disposing of any
medical supplies which could not be thoroughly cleaned.

However, three
weeks after the woman was discharged, a new case of K. pneumoniae was diagnosed in a 34-year-old cancer patient who had
never had any contact with her.

Doctors at the
hospital were unsure whether the two cases were related. For other bacteria, the
hospital would use a technique called pulsed-field gel electrophoresis to
differentiate between strains. But due to the nature of K. pneumoniae, that
technique was unhelpful.

Despite the
hospital's best efforts, the infection spread to another 15 patients over
the course of five months. Initially, it was confined to the intensive care
unit, but it soon spread to the rest of the hospital. By now, the hospital was 'cohorting',
ensuring staff treating the infected patients were not working elsewhere, and
employing extreme disinfecting techniques, even fumigating entire rooms with
hydrogen peroxide gas.

Dr Julie Segre,
a genome researcher at NIH, suggested that sequencing the entire genome of the
first patient's bacteria would allow a comparison with the genome sequences of
bacteria from other patients, mapping the spread of the disease.

Sequencing demonstrated
that the first patient was responsible for all subsequent infections, transmitting
the bacteria from her lung and throat on three separate occasions.

'It is very
difficult to contain an epidemic once these kinds of organism are introduced
into the hospital environment', said David Henderson, NIH Clinical Centre's
deputy director for clinical care. 'They become endemic and part of the
hospital flora'.

The bacteria
from the patient's lungs had a difference of seven base-pairs out of six
million from those her throat, allowing the researchers to make a detailed
analysis how it had spread.

Every patient in
the hospital was also tested for the bacteria, revealing eight carriers who
showed no symptoms, explaining the apparent gaps between infected patients. The
contamination was eventually tracked to the plumbing connected to the first patient's isolation
unit, and a ventilation machine which had not been successfully disinfected.

'We had never done this type of
research in real time', Dr Segre said.

The sequencing pointed to a source
of infection that was unforeseen, and showed that the bacteria could survive
undetected for an extremely long time. The research could lead to future use of
genome sequencing in hospitals to prevent the spread of other infectious
diseases. In the USA, more than 99,000 people die every year from
hospital-acquired infections.

'It's great to
see this study', Professor Sharon Peacock,
from the University of Cambridge, UK, told New Scientist. 'It's going
to lead to a step change'.

Currently, most
hospitals in the UK do not have the expertise or resources to carry out the
analysis in-house and some researchers suggest an online database of bacterial
genomes would help in the future.

'The quality
of answer will only be as good as the database', Professor Peacock commented.