The Centers for Disease Control and Prevention is requesting $40 million in its fiscal year 2014 budget to build advanced molecular detection and informatics systems for tracking infectious disease outbreaks.
The CDC says it currently lacks the molecular sequencing tools and bioinformatics capacity to keep up with emerging threats like the antibiotic-resistant bacteria strains plaguing U.S. hospitals and the H7N9 influenza that recently evolved in China.
“CDC needs next generation diagnostics to find and stop killer microbes before they spread,” said CDC Director Thomas Frieden, MD, in a briefing on the proposal. “It used to take weeks to months to sequence a genome of a bacteria or virus.” Today’s technology — cousins of the same high-throughput sequencing tools bringing down the cost of humane genome analysis — “can do that in just a few hours,” he said, helping researchers identify pathogens and determine the scope of their resistance.
Investing in better systems now would reap dividends down the road, he said.
The advanced molecular detection proposal is envisioned as part of a modernization of state and national CDC informatics and genomics systems, with $40 million requested for systems modernization being part of a $432 million request for programs on infectious disease monitoring and prevention.
That $432 million would represent a $70 million increase over the fiscal year 2012 allocations (fiscal year 2013 is technically still being funded out in a piecemeal fashion, under the federal sequester) and about $51 million would come from the Affordable Care Act’s $18.7 billion Prevention and Public Health Fund.
Even though the agency’s proposed 2014 budget as a whole, at $6.6 billion, would be a $270 million decrease from fiscal year 2012, the CDC is trying to prioritize infectious disease tracking modernization at a time when infectious pathogens are growing more complex.
There are currently five potentially life-threatening microbes that are nearly resistant to all available drug treatments, notably the carbapenem-resistant Enterobacteria (or CRE) that kills nearly half of all patients whose bloodstream get infected with it, according to the CDC.
Bacteria like CRE and C. difficile have troubled for hospitals, where the aim for sterile environments, the coming-and-going of thousands of people and broad-spectrum antibiotic use have lead to persistent infection challenges. About 100,000 Americans die from hospital-acquired infections annually — compared to some 33,000 annual deaths from motor vehicle accidents and about 31,000 deaths from gun violence.
While hoping for Congressional funding to modernize monitoring systems to track and help thwart pathogens like CRE, the CDC is emphasizing the need for best practices at hospitals, as well as local public health and internal monitoring.
The CDC is also trying to expand its monitoring of foodborne pathogens, in an increasingly globalized food chain — with Illinois soybeans and pork being exported to China, for instance, and Europe importing Chinese strawberries, the suspected cause of a norovirus outbreak that affected some 11,000 German school children last October.
About 48 million Americans get sick from contaminated food each year, at a cost of $77 billion in healthcare costs and lost productivity, according to the CDC.
According to federal data recently sifted through by the Environmental Working Group, national sampling by the CDC, FDA and USDA in 2011 found high levels of some form of antibiotic resistant bacteria on 81 percent of ground turkey, 55 percent of ground beef, 61 percent of pork chops and 39 percent of chicken breasts, thighs and wings. About 10 percent of both the ground turkey and chicken samples had anitbiotic resistant strains of salmonella, and over 50 percent of the chicken samples had antibiotic resistant E. coli.
The CDC’s interest in better informatics for tracking and modern sequencing tools for identification is coming along with a sort of paradigm shift in medical thinking on infections.
As Vincent Fischetti, a professor of bacterial pathogenesis and immunology at Rockefeller University, told NPR’s Science Friday recently: “What we really need are diagnostics that will tell you as soon as you walk into the hospital what organism is causing the infection, and then you can use a very specific antibiotic to kill that organism. That way you avoid the whole problem of killing lots of organisms — which are really necessary for health and wellbeing, and cause other problems when you start destroying your whole flora.”