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Genetic Analysis Improves Medicine's Response to Infectious Outbreaks

DNA Sequencing Speeds Tracking and Containment Bacterial Contagions


Genetic Analysis Improves Medicine's Response to Infectious Outbreaks

MRSA, 20,000x Maginfication

Janice Haney Carr, CDC
Updated February 28, 2013

There’s a lot of discussion about the impact of high throughput DNA sequencing technology on personalized medicine, individual DNA analysis is being used to determine a person’s risk for certain diseases, responsiveness to particular treatments, and other health related individual genetic traits. However, this technology is also bringing about real improvements in other areas of healthcare. In particular, it is changing the approach to tracking infection routes of pathogens and, in one recent case, found a hospital staff member was the source for a series of patient infections.

Tracking the Infection Path

Humans have about 1,000 times more DNA than bacteria, so as it is getting to point that sequencing an individual’s DNA is just $1,000, you can sequence a bacteria’s DNA for less than $100. This cost effectiveness of high throughput sequencing enables investigators to sequence large numbers of samples from multiple patients involved in an outbreak. This highly accurate information about the specific strains enables them to identify and track small differences in the DNA of the variants present in different patients, so they can determine which ones are more closely related and who likely infected who.

Genetics Can Identify the Most Effective Antibiotic Faster

As I mentioned in a previous article, researchers used DNA sequencing to analyze samples from an outbreak of antibiotic-resistant Staphylococus aureus (MRSA) that occurred in a neonatal unit of a hospital in England in 2009. Through genetic analysis the researchers were able to track the course of patient-to-patient infection. As a result, they found that one of the patients was infected from a completely separate source. Also, they identified the antibiotics that were eventually found to effectively treat the infections. The analysis showed that, if high throughput DNA sequencing would have been available at the time of outbreak, the outbreak would have been contained more quickly since the babies would have been treated with the right antibiotics more quickly.

Tracking Down the Source of the Infections

More proof of the effectiveness of using DNA sequence to track hospital infections comes from another study published at the end of 2012 that also analyzed a series of cases of MRSA in a UK hospital neonatal unit. Over a 6 month period 12 infants had come down with MRSA. However, in this case, the hospital had not been able to track down the source, and wasn’t even certain it was coming from within the hospital. By comparing the DNA sequencing isolated from various patients, the researchers were able to prove that the outbreaks were related. They also linked additional cases in the community—parents and family members of infected infants—to the same hospital outbreak even though some of these other children came down with MRSA after being released.

The most interesting development in this study, however, was that they identified a staff that was carrying the bacteria without symptoms, and that this staff member reintroduced it into the neonatal unit after a deep clean was run to try to eliminate it from the facility. Treatment of this staff member eliminated further cases. The authors of this study point out that, "Rapid sequencing would have confirmed the outbreak…close to the start point, and routine whole-genome sequencing of MRSA from all new cases…would have rapidly drawn links between the special care baby unit and the community."

Out of the Hospitals and Into the Streets

Tracking infections paths using DNA sequencing is not limited to small hospital outbreaks of MRSA. As the study above shows, infected can be tracked into the broader community outside the hospital. Another recent study looking at tuberculosis infections of 254 patients in the UK Midlands demonstrates the power of applying DNA sequencing to analyze more broadly infection epidemiology.

The researchers doing this work identified 11 different infection clusters—groups of individuals infected from a common source. Three of the clusters were linked to schools, and each of the non-school clusters but one seemed to constellate around a single super-spreader. They were actually able to determine who two of these super-spreaders were, and confirmed that they had untreated tuberculosis for several years. This is the sort of analysis during an outbreak that can help with rapid identification of transmission routes to more quickly halt the spread of the disease.

Change Comes Slowly

The authors of all of these studies point out how the rapid reduction in cost of high throughput sequencing over the last couple of years finally makes this sort of analysis feasible in real time during outbreaks. However, in a recent article in Science, Mark Walker and Scott Beatson point out that there are still a lot of technology impediments preventing the whole scale adoption of these methods in many hospitals.

While DNA sequencing has become less expensive, the methods are technically more complex than streaking samples on a petri dish, as is done for traditional microbiological analysis. Preparation of the samples for DNA sequencing requires time and expertise to generate and analyze genetic data on a large scale, as well as equipment which most healthcare facilities don’t have. Despite the fact that these techniques could transform the control and treatment of infectious disease outbreaks, it may be some time before they can be adopted as part of routine healthcare practices.

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