Friday, April 18, 2014

UPDATE: Rapid Tests for Ebola Virus Detection Halted Due to Lack of Funds

We recently blogged that Corgenix was developing a rapid test for the detection of Ebola virus.  However, it has been reported that their efforts are now stalled due to a lack of funds. This news could be further bad news for the Ebola outbreak in West Africa which began around March 25th. Ebola hemorrhagic virus has killed over 115 people in three different countries in West Africa. This infectious disease causes severe internal and external hemorrhage, organ failure, immune system breakdown and finally kills over 90% of its victims. With no vaccine or treatment developed so far, this dormant virus which is always present in Africa pops up almost every year.

It is believed that it infects the fruit bat which is a common food of West Africans. People get infected with the virus when they eat this fruit bat and it starts spreading rapidly from one person to another through contact. According to Dough Simpson, the Chief Executive of Corgenix, virus is spreading rapidly because it is taking time to diagnose. He stated that Corgenix has developed a new rapid test which will diagnose the disease in less than 15 min but, the work has been stalled due to lack of funds.

Currently, Ebola virus is spreading rapidly because the blood samples of those suspected of infection is sent to Europe for testing and it takes over 10 days for the reports to come back. By which the infection has spread to the next person or the suspected dies. The test that Corgenix has developed requires blood sample to be applied on a strip and it displays the result as positive or negative, much like a pregnancy test.

Outbreaks of Ebola usually occur when someone eats an infected fruit bat or other animal carrying the disease, which then spreads quickly through human populations via contact with someone who is infected, making quarantine essential to controlling the spread of the virus.

The most recent outbreak of Ebola, which began March 25, has killed more than 115 people. The disease has a 90 percent mortality rate, according to the federal Centers for Disease Control and Prevention. The last time this strain of Ebola broke out was in 2009, according to the CDC.

The rapid testing method being developed by Corgenix can help control outbreaks at the outset, Simpson said. Because Ebola only breaks out every few years, it can be difficult to contain because health-care workers usually assume that patients exhibiting symptoms have the much more common malaria and treat for that, which does not require quarantine.

After malaria, the next most common disease with the same symptoms is Lassa fever, for which Corgenix also produces a rapid test. Lassa can be cured using a cocktail of dangerous but effective drugs, Simpson said.
After receiving a $600,000 grant in 2010 from the National Institutes of Health, Corgenix was able to adapt its Lassa fever test to Ebola, but the grant ran out before the test could get through the necessary regulatory testing, Simpson said. The company has since applied for other grant funding to finish the work, but as yet has had no luck obtaining more money.

Corgenix must test its products on dead strains of the virus, since it does not have high enough security clearance to handle live strains of Ebola. Facilities must be rated Biosecurity Level 4 to handle live strains of Ebola. Only 15 of these facilities exist nationwide, and none is in Colorado. Corgenix is a Biosecurity Level 2 facility.

The disease also is relegated to a small, oft-forgotten part of the world, but with the increased mobility of people and products it eventually could spread to more developed nations. What's more, the U.S. government is worried that the virus could be weaponized, Simpson said.

Kathleen Sebelius, former U.S. secretary of health and human services, stressed increased globalization as a health concern in a recent speech at the University of Colorado-Boulder.

Actions and outbreaks in one part of the world have the potential to impact everyone, Sebelius said during remarks at the Conference on World Affairs earlier this month. Everyone is connected by food, water, air, trade and travel, she said.

"In this 21st-century world, we're no longer separated by two oceans," she said.

While tragic, every outbreak brings with it a new opportunity to bring Ebola to the forefront and obtain new grant funding.

"This outbreak reinforces the importance of developing and testing a rapid Ebola test," said Robert Garry, professor of microbiology and immunology at the Tulane University School of Medicine, in an email. "In patients demonstrating fevers, we need the ability to not only screen for Lassa, but also Ebola. The (Viral Hemorrhagic Fever Consortium) is expanding on our existing diagnostic testing foundation to advance Ebola testing in the same way we've been successful with the development of the rapid test for the Lassa virus."

The Viral Hemorrhagic Fever Consortium is an international group that is working to win approval for rapid tests for Ebola and Lassa, among other diseases. Nine organizations in addition to Corgenix are involved. Last month, the consortium sent experts to Guinea to help deal with the Ebola outbreak.

In Africa, the European Medicines Agency standards are used to determine whether a product is ready to be commercialized, rather than standards set forth by the U.S. Food and Drug Administration, Simpson said. The Lassa fever test produced by Corgenix is approved by the European Medicines Agency, but the Ebola test has yet to be approved, he said.

Ebola, while gory and deadly, isn't a top-of-mind disease in a world where conditions such as HIV and cancer still are incurable. Finding grant money to research ways to keep the disease under control is hard, Simpson said, but his company isn't giving up.

Although the going is slow, Simpson is sure the tests eventually will be approved and made available to those who need them.

"It is so rare, but when it pops up, it's ugly," he said. "It's going to come popping up again. We want to advance (rapid testing) to the stage where it can be used next time."

CDC: Foodborne Illness in the U.S. Not Getting Better

The Centers for Disease Control and Prevention today released their annual survey of foodborne illnesses in the United States, and the news is, well, not great. In the words of the press announcement they sent out to announce the data release: “limited progress.”

The survey — technically the Foodborne Diseases Active Surveillance Network, but usually known as FoodNet — doesn’t cover the entire US; it’s a representative sample drawn from 10 sites in nine states where the CDC already has arrangements with epidemiologists and laboratory personnel. Those 10 sites, most of them at state health departments, cover 48 million people, or about 15 percent of the US population. So among that slice, in 2013, there were:
  • 19,056 lab-confirmed foodborne illnesses,
  • 4,200 of which were severe enough to cause the person to be hospitalized,
  • and 80 of which caused the person’s death.
(For context, the CDC’s extrapolation of foodborne illness nationwide, made in 2011, was 48 million illnesses, 128,000 hospitalizations and 3,000 deaths.)

The agency compared the 2013 numbers against two sets of data, one set taken covering 2010-12 and the other 2006-08. Its summation, from its report in its weekly publication MMWR:

Compared with 2010–2012, the estimated incidence of infection in 2013 was lower for Salmonella, higher for Vibrio, and unchanged overall. Since 2006–2008, the overall incidence has not changed significantly. More needs to be done.

Here’s a handy cheat sheet for the major fooodborne organisms, distributed by the CDC. Note that none of the smileys are actually smiling:

Click image for a larger view.

That graphic is a little misleading in that it lists the problem organisms alphabetically. Of the six organisms, Salmonella causes the most illness, at 38 percent of the reported infections; Campylobacter comes second, at 35 percent. Vibrio, which had the largest increase, causes only 1 percent of infections.

If you know anything about bad bugs and food, those first two may sound familiar; they’re often associated with chicken, the meat that we in the United States eat the most of. (Vibrio is most associated with shellfish.) Why would two chicken-related organisms be problematic? The CDC report provides a clue: There is no federal standard for how much Campylobacter can be present on chicken, and the federal standard for the presence of Salmonella has not kept up with changes in what chicken Americans buy. From the MMWR:

In 2011, USDA-FSIS tightened its performance standard for Salmonella contamination of whole broiler chickens; in 2013, 3.9% of samples tested positive. Because most chicken is purchased as cut-up parts, USDA-FSIS conducted a nationwide survey of raw chicken parts in 2012 and calculated an estimated 24% prevalence of Salmonella.

Tightening standards for whole birds when people buy cut-up ones sounds like a chicken version of looking under the streetlamp for the keys you dropped, because the light is better there. But to be fair: The USDA apparently noticed this mismatch and, last year, proposed a Salmonella action plan, including an examination of contamination issues for chicken parts, and also is working on new Campylobacter standards. (I’ll try to do more on this after the holiday.)

The needle didn’t budge either for E. coli infections from the severe, toxin-producing strain O157:H7, which causes a kidney-overload syndrome that can kill young children. (If you’ve been reading for a while, you might remember that O157:H7 has been considered a zero-tolerance “adulterant” in food since 1994, but other similar “STECs” — toxin-producing E. coli strains — only got that regulatory status in 2011.) . Reacting to the numbers, the Consumer Federation of America said in a statement:

Progress on reducing illnesses from E. coli O157:H7 looks to have stalled and in fact, may be trending back upwards after several years of success. Also troubling is that illnesses from non-O157:H7 STECs continue to trend upwards. Illnesses from E. coli O157:H7 and non-O157 STECs have shown no significant change when compared to the 2006-2008 baseline. In addition, for the third year in a row, the incidence of illnesses from non-O157 STECs is higher than illnesses from E. coli O157:H7.

Finally, a troubling issue emerged during the CDC’s press briefing, mentioned by Dr. Rob Tauxe, deputy director of the agency’s foodborne-illness division. To get diagnoses made more quickly — and thus get patients medical help faster — public health labs have begun using rapid tests that recognize a molecular signature, instead of the traditional culture-based tests that grow the bacterium on a dish and test it. This has a significant downside: No organism means no ability to do the “DNA fingerprinting” that the public health system relies on for PulseNet, a crucial tool that can link infections that occur many miles away from each other. Reacting to that, Caroline Smith DeWaal of the Center for Science in the Public Interest said in a statement:

It is critically important that CDC develop a plan to address the increasing use of diagnostic tests that don’t use lab cultures. Otherwise the trend of declining reporting of outbreaks may continue—not because fewer people are getting sick, but because state health departments and CDC cannot track the outbreaks.

I’ll add one thing to that. Not having a cultured organism also means losing the ability to detect when the foodborne illness is antibiotic-resistant, because resistance assays at the moment rely on having living bacteria. Antibiotic resistance is an increasingly important issue for food production; the now year-long outbreak in chicken from Foster Farms, which has racked up 524 infections in 25 states, involves a Salmonella that is multi-drug resistant. No longer being able to track resistance could mean completely losing track of foodborne epidemics.

We know this can happen, because it already did happen, for gonorrhea, which currently is veering toward untreatability all over the world. As I reported two years ago at Scientific American and here, multi-drug resistant gonorrhea got out ahead of us because public health’s switch to inexpensive rapid tests for STDs sacrificed the ability to examine whether the bacterium’s resistance profile was getting worse. For that to happen to foodborne illnesses as well would be a backward step for public health.

Source: Wired

CWRU Grad Wins $100,000 for Malaria Diagnosis Device

A former Case Western Reserve University graduate student has won $100,000 in a national business competition to help fund the Cleveland-based biomed startup he co-founded, which is developing a test that can rapidly diagnose malaria. The award, funded by Under Armour founder Kevin Plank, was announced Friday.

In 2012, John Lewandowski and Case malaria researcher Brian Grimberg formed Disease Diagnostic Group to develop a handheld device which uses magnets and simple optics to pick up even tiny amounts of the malaria parasite in a patient’s blood, promising to save millions of lives a year.

The Cupid’s Cup Business Competition, held at the University of Maryland, is an annual competition awarding the work of undergraduate, graduate and recent graduate student entrepreneurs. The competition is chaired by Plank, who is a 1996 graduate of the school.

Lewandowski, 23, won $75,000 and was awarded an additional $25,000 in exchange for a piece of the company, which he accepted. Lewandowski also won $5,000 as the audience favorite, decided by text vote from about 1,000 people attending.

"I've been traveling for the past eight weekends for business plan competitions, and we've actually won all of them," he said. "This is by far the biggest one."

Lewandowski, a Cleveland native who is now a graduate student at Massachusetts Institute of Technology, graduated in 2012 from Case with bachelor’s degrees in mechanical engineering and economics, and a master’s degree in engineering and management.

Working with Grimberg's original concept in CWRU's [think]box fabrication lab, Lewandowski helped shrink down the size of the device to make it practical for use.

The company’s test, called the Rapid Assessment of Malaria device, or RAM, has several advantages over existing methods of testing for the disease. Traditionally, doctors use a microscope in a lab to examine the blood for signs of the malaria parasite, but this can be expensive, time-consuming, and difficult to deliver to rural areas where the disease is most common.

Other rapid tests that use a dipstick to pick up proteins in the blood, much like a pregnancy test, can’t detect very small numbers of the parasites. Picking up parasites at low levels -- when patients often still feel well but are carriers of the disease and infecting others -- is key to eradicating malaria, which kills more than 600,000 people a year.

The RAM detector picks up iron-rich crystals shed by malaria parasites after they eat hemoglobin, the oxygen-carrying protein in red blood cells. The iron, which is a metal, is magnetic, and can be manipulated within a blood sample and detected in characteristic patterns when viewed through a laser light.

The detector's results take less than a minute and cost about 20 cents, cheaper than other rapid tests, which can cost about 50 cents. Lab tests show the device can pick up as few as 17 parasites in a microliter of blood, compared to about 100 parasites per microliter for microscopes and other rapid tests. Accuracy is also better, according to company lab tests: 97 percent accuracy for the RAM compared to about 85 percent accuracy for other rapid tests and 50 percent for microscopes.

Last summer, the company successfully raised the $250,000 necessary to start field trials of the device, which are now underway in Peru and India.

"Right now we're at the end of the prototyping phase and looking to partner with a manufacturer that can help us produce a product that can be scaled," Lewandowski said. "Things have really started to pick up. As we progress the pressure builds, but that's a good thing-- it makes me want to succeed even more."

Picture: John Lewandowski, left and Case Western Reserve University malaria researcher Brian Grimberg, right, formed Disease Diagnostic Group in 2012 to develop their rapid diagnosis device for malaria. Lewandowski, now a graduate student at MIT, now has $100,000 to put towards their business plan after winning the 2014 Cupid's Cup competition, which awards student entrepreneurs. (John Kuntz/The Plain Dealer)

Monday, April 7, 2014

CDC to Use DNA Mapping to Fight Food Poisoning

Chances are you've heard of mapping genes to diagnose rare diseases, predict your risk of cancer and tell your ancestry. But to uncover food poisonings?

The nation's disease detectives are beginning a program to try to outsmart outbreaks by routinely decoding the DNA of potentially deadly bacteria and viruses.

The initial target is listeria, the third-leading cause of death from food poisoning and bacteria that are especially dangerous to pregnant women. Already, the government credits the technology with helping to solve a listeria outbreak that killed one person in California and sickened seven others in Maryland.

"This really is a new way to find and fight infections," said Dr. Tom Frieden, director of the Centers for Disease Control and Prevention. "One way to think of it is, is it identifying a suspect by a lineup or by a fingerprint?"

Whole genome sequencing, or mapping all of an organism's DNA, has become a staple of medical research. But in public health, it has been used more selectively, to investigate particularly vexing outbreaks or emerging pathogens, such as a worrisome new strain of bird flu.

For day-to-day outbreak detection, officials rely instead on decades-old tests that use pieces of DNA and aren't as precise.

Now, with genome sequencing becoming faster and cheaper, the CDC is armed with $30 million from Congress to broaden its use with a program called advanced molecular detection. The hope is to solve outbreaks faster, foodborne and other types, and maybe prevent infections, too, by better understanding how they spread.

"Frankly, in public health, we have some catching up to do," said the CDC's Dr. Christopher Braden, who is helping to lead the work.

As a first step, federal and state officials are rapidly decoding the DNA of all the listeria infections diagnosed in the U.S. this year, along with samples found in tainted foods or factories.

It's the first time the technology has been used for routine disease surveillance, looking for people with matching strains who may have gotten sick from the same source.

If this pilot project works, the CDC says it sets the stage to eventually overhaul how public health laboratories around the country keep watch on food safety, and to use the technology more routinely against other outbreaks.

"Genome sequencing really is the ultimate DNA fingerprint," said George Washington University microbiologist Lance Price, who uses it to study the spread of antibiotic-resistant bacteria and says the CDC's move is long overdue.

Especially in foodborne outbreaks, the technology will increase investigators' ability to nab the right culprit, he said. The faster that happens, the fewer people may get sick.

"This is going to change everything as far as source attribution," Price added. "Recalls are expensive, the industry doesn't like them," and they've got to be accurate.

Today's standard tests sometimes miss linked cases or provide false leads. For example, U.S. officials in 2012 initially thought a salmonella outbreak in the Netherlands, associated with smoked salmon, was linked to cases here. Later sequencing showed the bugs were different.

"The current methods of subtyping salmonella aren't very good," said epidemiologist David Boxrud of the Minnesota Department of Health, part of a pilot Food and Drug Administration network that has begun sequencing that germ and certain others when they're discovered in food. State labs in Arizona, Florida, Maryland, New York, Virginia and Washington also participate.

Sequencing also promises to reveal drug resistance and how virulent a germ is more quickly than today's tests, and track how it's spreading from one person to another through tiny genetic changes that act like footprints.

Key to making it work is the computing power of a massive federal database being used to store the gene maps, said Duncan MacCannell, the CDC's senior adviser for bioinformatics. It's one thing to analyze bacterial DNA culled from a few dozen sick people during an outbreak, and another to compare samples from thousands.

Until recently, the CDC didn't have the "tools and approaches to make sense of this much data," he said.

The listeria project began as officials were investigating some sick Maryland newborns and their mothers. Genome sequencing showed those cases were linked to a California death, helping investigators determine which foods to focus on, said Dr. Robert Tauxe, CDC's leading foodborne disease sleuth.

Standard tests prompted recall of the FDA's suspect, a brand of Hispanic-style cheese. Last month, the government announced that sequencing also confirmed listeria from the recalled cheese matched germs from the patients.

"We expect to be able to match more and more of what we find in people to what we find in food," as the project grows, Tauxe said.