Pathogen outbreak controlled by genome sequencing
20 Nov 2014
A pathogen outbreak at a hospital in 2011 was controlled by real-time genome sequencing, a new report suggests.
Researchers from the University of Birmingham, University of Warwick, and the National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre have published details of how whole genome sequencing was used to control an outbreak of Acinetobacter baumannii at Queen Elizabeth Hospital Birmingham in 2011 following the admittance of a military patient from Afghanistan.
“Whole genome sequencing can be applied in a helpful timeframe to track and control the spread of drug-resistant hospital pathogens
Lead author Mark Pallen
Acinetobacter baumannii is a multi-drug resistant pathogen found in hospitals around the world, emerging recently as a significant threat to casualties in the Iraq and Afghanistan wars as it affects patients who suffer from trauma and burns.
The outbreak at the Queen Elizabeth Hospital in 2011 lasted for 80 weeks and was caused by a novel strain of the bacterium that had not previously been observed in the region’s hospitals.
Mid-way through the outbreak, researchers reversed their traditional pathogen containment strategies and employed whole genome sequencing in an effort to control the outbreak.
By sampling patients and the environment, the researchers were able to identify 74 patients belonging to the outbreak and then determined the detailed genetic makeup of the bacteria carried by each of these patients and used this data, alongside information about the ward that the patients were housed in, and the date of their first positive tests, to identify nearly 70 possible transmission events.
Armed with this information, the researchers were able to pinpoint specific areas of transmission within the hospital - deep-cleaning these transmission sites and eventually closing the pathogen outbreak in May 2013.
“We have demonstrated how whole genome sequencing can be applied in a clinically helpful timeframe to track and control the spread of drug-resistant hospital pathogens. In this case, it helped understand and control what was probably [the] longest running A. baumannii outbreak ever seen in this country,” said lead author of the study Mark Pallen from the University of Warwick.
