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CDC Plans to Map DNA of Disease-Causing Viruses

Courtesy Centers for Disease Control and Prevention
A tiny gene sequencing chip can help to identify the DNA of a virus in just three hours, compared with what previously took months.

Many public health experts see the Centers for Disease Control and Prevention as the premier disease detection agency not just for the United States but for the entire planet.

Yet when it comes to employing the fastest and most precise method of spotting outbreaks of illness, the CDC is no longer at the cutting edge — and won’t be for years. Centers for Disease Control and Prevention Director Thomas Frieden along with public health and provider groups want to turn that around by investing in a sophisticated technology called “advanced molecular detection” that determines the genetic map of the viruses, bacteria and parasites that cause disease.

The effort began paying off early this year. Appropriators for the first time in several years decided to rewrite Labor-HHS-Education spending provisions. In doing so, they included $30 million for the AMD technology in the omnibus spending measure funding the government through the end of fiscal 2014.

But Frieden must still persuade lawmakers to continue such annual funding for the five-year program for four more years. And he’ll be doing it even as he seeks additional funds for other programs. The Atlanta-based CDC director was in Washington last week to help present the administration’s fiscal 2015 budget proposal.

Advocates make the case that without action to boost U.S. technology to combat dangerous diseases, there will be more patients to treat who didn’t need to get sick, more lives needlessly lost and health spending that didn’t have to occur. It also means a loss of income to families and businesses that could have been avoided.

And the lag in technology is coming at a bad time, Frieden said during an interview — just as a retreat is under way in the great medical advances against infectious disease.

Deadly bacteria are becoming increasingly resistant to antibiotics with no quick way to know how widely that is occurring, Frieden said. That includes a strain called “the nightmare bacteria,” he said.

It’s a bacteria that’s resistant to just about all antibiotics and spreads diseases not only among the same organisms but jumps from species to species, said Frieden. Antibiotic resistance “threatens to take routine infections and make them untreatable,” he warned.

Advanced molecular detection is seen as key. As part of President Barack Obama’s fiscal 2015 budget proposal, Frieden wants to widen the impact of the technology and to improve protection against antibiotic resistance and other disease outbreaks in a variety of other ways through a new “global health security” initiative.

The sums involved aren’t major — and the threats they address are. But in an era of competing budget demands and tight caps on discretionary spending, there’s no certainty he’ll get the money.

Other obstacles also must be overcome before the CDC gets back to the cutting edge of disease detection.

Public health labs say they’ll need a more sophisticated workforce at a time when training funds are scarce. Also, to be able to make sense of the gobs of genetic data they’ll be getting, labs will need a reference library that in turn must build up its own genetic profiles of individual diseases.

That’s the case so a match can be made identifying a particular medical condition. Public health officials also may have to address concerns that advanced molecular detection could unintentionally weaken the existing system for monitoring the outbreak of foodborne illnesses.

AMD at Work

The viruses, bacteria and parasites that cause disease each have their own individual genetic makeups. Advanced molecular detection is used to determine what they are.

It does so by analyzing a small sample of virus or bacteria, for example. It prints out a sequence of the genes in the sample involved. That allows a precise match to a particular medical condition.

Also, the data can be made available within hours to the “bioinformatics” specialists who have the expertise to interpret it. These “rapid gene sequencing” techniques can be applied without the painstaking culturing of samples in labs over a period of days or weeks. It also can quickly determine whether bacteria is drug resistant — speed that could save thousands of lives, officials say.

“Imagine putting together a 10,000-piece jigsaw puzzle with the speed you could normally do a 100-piece puzzle — apply that to infectious disease control and that’s AMD at work,” says a CDC fact sheet on the technology. “Now imagine, while disease is spreading and people are dying, trying to put a 10,000 piece puzzle together when key pieces are missing. That’s what many CDC scientists are struggling against today.”

Investing in AMD “would bring the U.S. public health system a more precise and accurate means to find smoldering disease outbreaks we are missing now, find disease outbreaks faster to protect communities, and stop threats in our food supply,” the fact sheet said.

The CDC says highly resistant bacteria in hospitals are creating constant concern, as are “killer microbes that jump from animals to humans, and new virulent pathogens emerging.” It estimates that 48 million Americans get sick from contaminated food each year at a $77 billion cost in health care expenses and workplace and other economic costs.

Flu costs businesses some $10 billion a year and, according to the agency, “five killer microbes and counting are nearly resistant to all available drug treatments.” Each year 2 million people in the United States get infections that are resistant to antibiotics and at least 23,000 die as a result, it adds.

But the problem could grow worse, the agency says, naming antibiotic resistance one of the top five health threats in 2014. But with advanced molecular detection, public health officials and health care facilities will be better able to track and stop the rise of drug-resistant infections, the agency says.

Playing Catch-Up

The CDC isn’t alone in making the pitch. A letter last year from 33 patient, provider and disease groups urged funding to replace “obsolete” technology, citing outbreaks such as the one of fungal meningitis from contaminated steroids that killed some 50 people and an outbreak of resistant bacteria at the National Institutes of Health Clinical Center that killed seven.

“We’ve been concerned for a number of years that CDC is falling behind,” said Scott Becker, executive director of the Association of Public Health Laboratories. He cited investments 10 to 15 years ago in a technology known as PCR and in the PulseNet food illness surveillance network as ones that kept the agency then at the cutting edge of disease detection, but no longer.

It isn’t so much that the CDC is behind other nations as it is that the technology isn’t being used when dangerous new threats are emerging, said Becker.

“It’s more that the microbes are ahead of us,” agreed Frieden. “The microbes are evolving really quickly.”

But Frieden acknowledged a “painful” story. “During the [2010] cholera outbreak in Haiti we were able to sequence the genome of the cholera bacillus, but we couldn’t interpret it. So we had to send it to Canada to have it interpreted,” he said. “You know, I got nothin’ against Canada, but I never ever want to have to send something elsewhere to have it interpreted. They were ahead of us with bioinformatics.”

But with funding in hand at least for the first year, Frieden expresses confidence the United States will be back at the cutting edge within five years with continued bipartisan support.

Becker said the change “can’t come soon enough” but warns it won’t be easy and that grants are needed to develop the necessary workforce expertise: “If you don’t have the workforce you’re always going to be behind.”

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