New whole genome capabilities are opening a wide window of molecular epidemiology, as heretofore unidentifiable genetic markers can reveal paths of transmission between patients and facilities in an outbreak.
In a fascinating bit of detective work, researchers revisited a 2008-09 outbreak of Carbapenem-resistant Klebsiella pneumoniae (CRKP) that moved across the continuum between all manner of facilities in the Chicago area. One of the original investigators, Mary K. Hayden, MD, an infectious disease physician at Rush University Medical Center, saved the isolates. The original outbreak investigation identified 42 patients with CRKP in 14 hospitals, two long-term acute care hospitals (LTACHs), and 10 nursing homes.
However, the path of transmission as the emerging pathogen moved between facilities was not completely understood. Enter the Center for Microbial Systems at the University of Michigan, which conducted whole genome sequencing on the isolates as described in a recent paper.1
“When we were first investigating this back in 2008-2009, we could tell from electrophoresis that it looked like there was a single strain that came into the region,” Hayden says. “But that was not a discriminating enough tool to differentiate among isolates that might have changed in small ways over time.”
With whole genome sequencing, the chromosome of the bacteria that is common across an outbreak can be broken down in much greater detail.
“It is both more discriminating and can tell you the timing — it can actually tell you, for example, whether a particular mutation occurred before another mutation,” she says. “You can track the changes over time.”
An isolate of a patient who was thought to have introduced CRKP to the region was analyzed by this new technique, clearly showing how transmission began.
“We had the isolate and included it in the whole genome sequence analysis,” Hayden says. “We could identify with that analysis that the patient was probably ‘patient zero.’ The whole genome sequencing method showed that the first patient entered the region right around the first part of the year in which we started seeing the isolates.”
With multidrug-resistant strains emerging and transferring between facilities with transferred patients, whole genome sequencing is a powerful addition to outbreak investigation.
“There was a situation at one acute care hospital where we identified five isolates within a very short period of time,” Hayden says.
“When we did the original investigation, we assumed that there was one introduction to the hospital and then four transmissions. They all looked the same by pulse field and they all appeared within a fairly short period of time.”
To their surprise, the whole genome sequencing showed that this cluster was comprised of three separate introductions of CRKP, with only two transmissions occurring in the hospital, she says.
“If we had that information back then, we might have been more aggressive about screening patients at the time of admission and taking precautions to prevent cross-transmission in the hospital,” says Hayden, who also directs the clinical lab at Rush.
“The extra step we could have taken is screening upon admission.”
Simlarly, the transferring institutions could be alerted to the problem, taking action to prevent transmission before other patients go on to seed infection in other facilities.
“It is really whole genome sequencing combined with the classical epidemiology,” she says.
For example, public health interventions could have been taken at a nursing home that was suspected as serving as a reservoir for the pathogen, she says.
“When we looked again, combining the epidemiology and the whole genome sequencing, we had enough evidence to identify that this nursing home may have been the initial incubator [of CRKP] rather than the LTACHs,” Hayden says.
In an interesting aspect of the study, Hayden and colleagues overlapped the new detailed isolates with their original investigation and case finding, watching the genetic changes that showed transmission as the outbreak unfolded in real time.
“Would it provide additional information in that moment — with just the isolates in real time? In fact, it did,” she says. “By the time we had the second or third isolate, there was substantial information provided by whole genome sequencing to be able to tell us where these came from. What I’m saying is, even if they came from three different facilities, you could see that they were related. And the way that they were related would allow you to identify the problem facility to investigate.”
The approach is ideal for tracking emerging pathogens in healthcare networks, but also could have utility in investigating outbreaks of established bugs.
“It’s more complicated when you have an endemic organism, but I think it could still be quite useful,” she says.
The equipment needed to perform whole genome sequencing is becoming more affordable, so that more teaching hospitals and public health departments may begin using the method for outbreak investigation. For example, one manufacturer has instruments that perform whole genome sequencing for less than $20,000, Hayden says.
“Yes, that sounds like a lot of money, but I’m the director of a laboratory and that is not a terribly expensive piece of equipment for a clinical laboratory in a university setting,” she explains. “The costs are really declining.”
Beyond outbreak investigations, detailing the whole genome of important pathogens will have other benefits, she adds.
“If you think about it, when you do whole genome sequencing you get information about resistance genes, virulence genes,” Hayden says. “It is a lot more information that might be useful to inform public health from an epidemiological standpoint.”