Real-time, whole-genome sequencing helps control hospital outbreak

A team of researchers used real-time, confocal laser-based, whole-genome sequencing to help control a drug-resistant pathogen outbreak in a hospital.

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A team of researchers at the University of Birmingham, the University of Warwick, and the National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre (all in England) used real-time, confocal laser-based, whole-genome sequencing to help control a drug-resistant pathogen outbreak in a hospital.

Related: First-ever stoppage of MRSA outbreak by gene sequencing technology

In their study, the researchers used whole-genome sequencing (which involved the Illumina MiSeq platform) to control an outbreak of Acinetobacter baumannii (A. baumannii) at Queen Elizabeth Hospital Birmingham in 2011. The outbreak began following the admittance of a military patient from Afghanistan with blast injuries and lasted for 80 weeks, making it one of the longest outbreaks ever described for this pathogen. The patient was carrying a novel strain of the bacterium that had not previously been observed in the region's hospitals. After first using traditional methods to try and contain the pathogen, the researchers decided to switch to whole-genome sequencing mid-way through the outbreak.

Whole-genome sequencing, which sequences an organism's entire DNA, is thought to be a promising new addition to the toolkit for controlling healthcare-associated infections (HAIs). Conventional methods are often applied retrospectively and yield limited information about a pathogen's DNA, making it difficult to compare whether patients are carrying the same bacteria and track transmission of outbreaks.

Sampling patients and the environment, the researchers were able to identify 74 patients belonging to the outbreak. They then determined the detailed genetic makeup of the bacteria carried by each of these patients and used this data, with 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 detailed information, the researchers were able to pinpoint transmission hot spots within the hospital, which included an operating theatre and a specialised bed for burns patients.

Deep cleaning of these transmission sites followed and new decontamination protocols were put in place by the hospital. In May 2013, the outbreak was declared closed.

Full details of the work appear in the open-access journal Genome Medicine; for more information, please visit

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