Using Genome Sequencing to Combat Health Care Outbreaks

Often people think infection prevention and control is just reminding people to wash their hands and disinfect things. While these are core components to infection prevention, another piece that people often fail to recognize is epidemiology. When the “prevention” aspect of our work has failed, we move to the “control” components. Controlling the spread of an infectious disease can be challenging, therefore, understanding the transmission dynamics and source of the infection is critical.

Hospitals can easily be amplifiers of disease. We’ve seen this in various outbreaks, from the severe acute respiratory syndrome (SARS) coronavirus outbreak in Toronto to the outbreak of carbapenem-resistant Enterobacteriaceae (CRE) related to duodenoscopes within the University of California, Los Angeles Medical Center.

Infection preventionist epidemiologists work hard to identify spikes in usual case counts or rapidly respond to single cases of unusual organisms. Unfortunately, identifying a source or transmission mechanism isn’t always that easy and we often don’t find the proverbial “smoking gun”.

However, a study assessed the use of genome sequencing in real-time as a tool to help give hospital epidemiologists and infection control an advantage against microorganisms. Investigators across several universities discussed how they employed the rapid and cost-efficient tool during an outbreak of Acinetobacter baumannii at the Queen Elizabeth Hospital Birmingham in 2011.

The source of the outbreak was found to be a military patient from Afghanistan who was being treated for a blast injury. This specific case is unique in that the outbreak lasted an incredibly long time—80 weeks, which is the longest ever studied for Acinetobacter baumannii.

The novel strain led to an outbreak that resulted in 74 secondary infections however, it was only through employing the whole genome sequencing in the middle of the outbreak that the research team found this.

The traditional control methods were originally put in place, but by switching to this more rapid and sensitive approach, they could easily identify patients with the exact organism that had been transmitted from the original patient. Moreover, this lent itself to environmental samples, so coupled with the specific genetic knowledge of the strain causing the outbreak, they were able to find 70 transmission events. From the operating room to the burn unit, the team learned exactly where this exact organism had been, allowing for more targeted control efforts.

By identifying the patients with that exact strain, control efforts could focus on those areas they had been and any movement that occurred. This then allowed for the targeted disinfection of those areas within the hospital and helped quell the outbreak in May of 2013.

The utilization of whole genome sequencing allowed for infection control methods to include those patients who might be colonized and not necessarily infected with such a specific strain.

This very specific knowledge helps reduce the burden on the infection control team, but also ensures that patients with these novel or resistant strains are monitored/treated appropriately. This study sheds light on the application of whole genome sequencing in infection prevention and control methods and how its employment during outbreaks can change the process for infection control and epidemiologists.