Friday, December 28, 2012

We Have Updated Our Rapid Micro Methods News Page!

Great news for those of you who follow our rapid micro methods news page! We have just competed the migration of all of our news articles into a more user friendly format, which is very similar to our current RMM blog. As of today, all of our 2012, 2011 and 2010 news articles and press releases are now available for your review. Using this new format, there are a number of novel features that you can now utilize:
  • Review a list of the most popular-read news articles
  • Send articles to other social networks
  • Provide your comments
  • And in a few weeks (after the new pages are indexed), you will be able to search the entire news archive 
Additionally, all of our future news articles will now be automatically uploaded to our Twitter and Facebook pages. If you haven't already done so, I encourage you to follow us on Twitter and/or Facebook for a "rapid" way to stay in touch with what's happening in the world of RMMs.

Please visit our updated News Page now by clicking on the link at the top of this page!

Friday, December 21, 2012

Bacteria Will Prevent the End of the World

It's December 21, 2012. The sun is shining in Florida and there are no earthquakes, asteroids, solar storms, colliding planets or planetary alignments. However, the temperature did dip into the 40's last night, and for some Floridians, that meant the end of the world as we know it.

During this year I have blogged on the advancement of rapid microbiological methods (RMM) and the introduction of novel technologies for the rapid detection of organisms in a variety of industry sectors, including pharmaceutical, environmental, clinical and food. For the most part, these systems are utilized to detect the microorganisms that can cause us harm and where they are coming from. And in light of today's supposedly end of the world prophecies, here are a few bad-bug scenarios worth noting:

1. Nickel-eating bacteria may have worsened the world's worst mass die-off by producing huge amounts of methane, a new study suggests. The study is the latest attempt to explain how most of the world's ocean species died off in just a few hundred thousand years at the end of the Permian era, about 250 million years ago. The researchers presented their findings earlier this month at the annual meeting of the American Geophysical Union. The study proposes that a series of steps caused the mass extinction, but that bacteria played a key role. First, massive volcanic activity in Siberia released nickel into the atmosphere, which somehow reached the ocean. As a result, populations of ocean-dwelling bacteria that use nickel in their metabolic pathway exploded, releasing huge amounts of methane into the atmosphere and depleting ocean oxygen levels as a byproduct of that metabolism. Because methane is a greenhouse gas, the catastrophic gas release trapped heat in the atmosphere and caused the mass extinction by making the climate uninhabitable.

2. As bacteria evolve to evade antibiotics, common infections could become deadly, according to Dr. Margaret Chan, director general of the World Health Organization. Speaking at a conference in Copenhagen earlier this year, Chan said antibiotic resistance could bring about “the end of modern medicine as we know it.”

“We are losing our first-line antimicrobials,” she said Wednesday in her keynote address at the conference on combating antimicrobial resistance. “Replacement treatments are more costly, more toxic, need much longer durations of treatment, and may require treatment in intensive care units.” Chan said hospitals have become “hotbeds for highly-resistant pathogens” like methicillin-resistant Staphylococcus aureus, “increasing the risk that hospitalization kills instead of cures.”

Indeed, diseases that were once curable, such as tuberculosis, are becoming harder and more expensive to treat. Chan said treatment of  multidrug resistant tuberculosis was “extremely complicated, typically requiring two years of medication with toxic and expensive medicines, some of which are in constant short supply. Even with the best of care, only slightly more than 50 percent of these patients will be cured.” Antibiotic-resistant strains of salmonella, E. coli, and gonorrhea have also been discovered.

“Some experts say we are moving back to the pre-antibiotic era. No. This will be a post-antibiotic era. In terms of new replacement antibiotics, the pipeline is virtually dry,” said Chan. “A post-antibiotic era means, in effect, an end to modern medicine as we know it. Things as common as strep throat or a child’s scratched knee could once again kill.”

The dearth of effective antibiotics could also make surgical procedures and certain cancer treatments risky or even impossible, Chan said. “Some sophisticated interventions, like hip replacements, organ transplants, cancer chemotherapy and care of preterm infants, would become far more difficult or even too dangerous to undertake,” she said.

All things considered, it looks like microorganisms can play a role in armageddon. Not so fast my friends. The folks at have put things into perspective. Here is an overview of their thoughts on how bacteria can actually prevent the apocalypse from happening....

Not all bacteria is of the flesh-eating, "kill it before it kills you" variety. Some of it is actually good for you. Maybe you've seen the commercials where it helps people's gastrointestinal flow, for instance.

But even more beneficial than that, there are some strains of bacteria that not only can perform massive, superhero-level feats, but are probably going to be what stands between us and an apocalyptic future. Here are six examples.

#1. Controlling the Weather

If you've ever been unlucky enough to get caught in a hailstorm then you probably know that it's pretty painful. And while at the time you may have been rhetorically asking the heavens why they were so insistent firing tiny balls of ice at your face, now you have an actual answer: Nearly 85 percent of all hailstones have bacteria at the center.

The bacteria is called Pseudomonas syringae and when it's kicked up into the air, it collects condensation fury, forming water droplets (or in the case of hail, painful pellets). Generally the moisture in clouds needs something to cling around in order to create precipitation, and the bacteria provide the perfect nucleus.

So how does this information help us? Well it could allow us to weaponize water, destroying the windshields of our most hated enemies. Or we could use it to stop droughts.

We know that this particular bacterium causes water to freeze about 7 degrees Fahrenheit higher than usual, which means it can create snow and ice in slightly warmer temperatures. For that reason, mountain resorts have been using Pseudomonas syringae to make fake snow since the late '80s. But for anyone who's not jetsetting to Aspen this winter, there are more practical applications as well. Scientists say it's possible that planting crops already infected with these bacteria may help overcome droughts by inducing rain.

The bacteria is whipped up into the air the same way the pollen of plants would be, except once it climbs high in the atmosphere, the Pseudomonas syringae encourages rain in the area. Even if you're not on board with the idea of genetically engineering plants to be infected with bacteria, researchers think that just planting crops that encourage the bacteria would have a similar effect. And likewise, planting crops that the bacteria doesn't like might encourage droughts. So there might come a day when solving the world's water problems is just a matter of ordering up some manipulative microbes.

#2. Colonizing Other Planets

An unspoken rule among party-goers is that anyone left at the end of the night helps to clean up a little, so naturally everybody tries to leave early to avoid dealing with the mess. Well what if we could apply that same lack of accountability to Earth? If we never solve the energy crisis and don't get a handle on greenhouses gases, it may be possible in the future to just leave for another planet. Surely we won't mess that one up, right?

Apparently, a bacteria called Deinococcus radiodurans is going to help us along the way. This organism, which is nicknamed "Conan the Bacterium" is famous for its ability to not die. It shrugs off an astronomical amount of radioactivity, up to 1.5 million Rads, which is equivalent to 1.5 million Teenage Mutant Ninja Turtles, or 3,000 times more radiation than it takes to kill a human. It's also about 750,000 times more than the maximum daily measured radiation on Mars. See where we're going with this?

You may know that "terraforming" is the process of making another planet, like Mars, more Earth-like before we even get there. Obviously that's difficult if not impossible if the work involves millions of humans in bulky suits and hundreds of ships taking them back and forth. But microbes like Deinococcus radiodurans open up the possibility of sending a bunch of them spilling out onto the Martian surface and letting them do the work for us. For instance, even if Mars had our atmosphere, we couldn't grow plants there because the soil is toxic. But we have decoded the genome of Deinococcus radiodurans, and therefore could one day engineer a version that would change the composition of the Martian soil, making it plant-friendly.

But there are broader applications; just examining the way the microbe resists damage from radiation tells us a lot about how to engineer other things to do the same (radiation is normally harmful because it damages DNA, and Deinococcus radiodurans has a mechanism for rapidly repairing that damage). We could theoretically do everything from engineering goods to survive the long trip through space to genetically altering the astronauts themselves to be impervious supermen or superwomen.

#3. Eating Battleships

The biggest problem with ships is that when they're old and unusable, there's nowhere to retire them other than the bottom of the ocean. The U.N. estimates that over 3 million ships are located on the ocean floor, with fewer than a thousand that anyone has any plans to clean up. And that's not even covering all the defunct oil rigs down there. As cool as it might be to go exploring sunken battleships on the bottom of the sea in search of treasures and corpses, what we really need is a way to clean up the mess.

Enter Halomonas titanicai, a bacterium that loves eating metal and could do all the cleaning up for us. The Titanic sank in 1912, where it sat undisturbed for over 70 years. Well, "undisturbed" isn't entirely accurate. During that time, a bacterium sprouted colonies all over the vessel and they are eating the ship. This bacterium adheres to metal, then create rust knobs which appear to be slowly devouring the ship. It's good news for anyone who is mildly interested in ocean health, but sadly, bad news for anyone who was substituting an old cruise ship for an actual relationship.

Because of the great work the bacteria is doing on the Titanic, researchers don't see any reason we can't use the same cultures to clean up other oil rigs and ships. Or, conversely, knowing exactly how the bacteria eats away at metal can inform how we build boats in the future so that they are stronger. By finding a way to prevent this bacteria from colonizing, we can ensure that oil rigs stay structurally sound for a lot longer. Then again, if one of them collapses and it's resistant to the bacteria, then we're right back where we started with steel trash on the floor of the ocean.

#4. Fixing Obesity

Your intestines play host to about 500 different species of bacteria, and that's a good thing because bacteria break down and absorb the food our bodies can't digest alone. The last thing anyone wants in their belly is all the food you ever ate ever, right?

Recently, scientists have found that when we eat a high-fat, sugar rich diet, we not only pack in the calories, we also encourage the growth of bacteria called Firmicutes in our intestines, which happen to love Pringles and Twix bars. They love fatty foods so much that they devour it, breaking the compound down until it is sure to be absorbed by the body.

In a study that changed the diet of lab mice from low-fat, plant based meals to fatty foods, the mice picked up a new set of bad bacteria overnight and started packing on the pounds. They even stayed fat after switching back to low-fat foods. So that's the bad news. Bad bacteria makes you fat. Here's the good news: Good bacteria makes you skinny! Surprise!

Daily intake of a unique lactic acid bacteria was shown to keep the fat-loving bacteria away, which is great news for people who despise the idea of working out. Scientists tested the effectiveness of Lactobacillus plantarum HEAL19 by feeding it to baby rats every day, even before they were born. Then those rats were fed some high fat, fast-foodish diet and despite enjoying fatty foods, the rats with the lactic acid bacteria living inside their gut stayed leaner.

So, the theory goes that by intentionally ingesting something Lactobacillus regularly and from an early age, you can allow this stuff to colonize inside of you like tiny but stern diet camp councilors that constantly keep obesity in check.

#5. Cleaning up Oil Spills

Thanks to recent oil spill tragedies, you might have already known that there's a bacterium that eats oil. What you probably didn't know was that the bacterium is called Alcanivorax borkumensis. It is pretty rare in unpolluted waters, but once an oil spill occurs, it shows up like a superhero. We'd equate it to Aquaman, but technically the bacteria is just a little bit better at its job. The microbes start multiplying quickly in the event of a spill, fattening themselves on oil ... but only to a certain point. The BP oil spill overwhelmed the existing oil-eating bacteria and they weren't nearly as helpful as they were for the Exxon Valdez spill in 1989. But some people think they have the answer to that problem. With fertilizer. Specifically, nitrogen and phosphorous. The same stuff that they're putting on the (nonorganic) crops that are feeding the world could also fertilize the bacteria that loves oil. Adding fertilizer to the water increases the size and number of the bacteria so there are more out there to cut through all that oil.

Still, the process hasn't exactly been tested in deep waters yet, and one of the main consequences could be an overwhelming amount of algae (which also loves fertilizer). That kind of thick marine vegetation could overpower more fragile species. Still, it's been proven to work well near shores and can still do a whole lot of good.

#6. Turning Greenhouse Gases into Bricks

We don't need to explain why CO2 is a problem for the environment right now -- it's why the nations of the world are scrambling to reduce emissions before we fry ourselves into a Venusian nightmare.

A lot of potential CO2/global warming fixes are on the table, but sometimes just overcoming your enemy isn't enough. Sometimes you want to destroy them and use pieces of them in your buildings and roads just to remind yourself how superior you are. Well it turns out we can do just that with carbon dioxide.

There are two ways that nature deals with CO2: either through photosynthesis in plants which turns out oxygen, or through bacteria which convert CO2 into solid calcium bicarbonate. That kind of "air into stone" transformation sounds like alchemy, but about 40 percent of the chalk cliffs in the world are created by carbon dioxide absorbing microbes. Not only are oxygen and calcium bicarbonate less threatening for humanity and for the world, they are also completely useful to us.

A group of Indian scientists have discovered bacteria capable of creating building materials out of the carbon dioxide in the air, essentially creating a chemical reaction that turns a gas into a separate, solid compound. A rock-solid compound.

We can use calcium bicarbonate in building materials, agricultural lime, the purification of iron and even antacid tablets. The group of scientists speculates that modern factories could include bacteria chambers to convert the CO2 before it leaves the building. This would allow a factory to produce massive stores of calcium bicarbonate while giving off only low levels of dangerous emissions, thus killing two birds with one chalky stone.

In Conclusion

So, there you have it. The world isn't coming to an end today, microorganisms may actually help us more than hurt us, and I have another year to blog about rapid methods!

Wishing you and yours a very enjoyable holiday season, and a very happy and healthy New Year!

Wednesday, December 12, 2012

Our Latest Newsletter is Now Available

Our final Newsletter of the year is now available for your review. The Newsletter will keep you informed of updates to our RMM News, Calendar of Events, Blog, Published References and RMM Technologies pages. 

To receive our Newsletter, please sign up by clicking on the following link: We will then email the Newsletter directly to your inbox!

Tuesday, December 11, 2012

Approval for Rapid Diagnostic for Foodborne Pathogen has Ramifications for Healthcare

A Philadelphia life science startup with a pocket-sized diagnostic assay for detecting foodborne pathogens has received accreditation from the Association of Analytical Communities for a test for bacteria most commonly found in chickens - Campylobacter, according to a company statement. The test has ramifications not only for reducing healthcare costs, but also for how healthcare providers identify hospital-acquired infections.

The Campylobacter bacteria affects 2.5 million people each year in the US.

Invisible Sentinel’s Veriflow test uses a molecular detection system designed to comply with stricter food testing standards. Its designed to speed up the time it takes to identify whether samples are contaminated. It is also intended to make it easier to use and more easily transported. The assay utilizes a PCR detection method coupled with a rapid, visual, flow-based assay that develops in 3 minutes post PCR amplification and requires only 24 hours of non-specialized incubation for maximum sensitivity. The Veriflow™ Campylobacter system eliminates the need for microaerobic chambers, gel electrophoresis or fluorophore based detection of target amplifications, and does not require complex data analysis.

Once the AOAC greenlights a performance tested method, it is recognized by the US Department of Agriculture, the Food and Drug Administration, certain European Union counterparts and other global regulatory agencies.

Ben Pascal, the CEO, said its manufacturing facilities in the University City Science Center is up and running and the company is talks with distribution partners in the US and Europe. The Campylobacter assay is the first in a suite of tests that are expected to be rolled out out next year for listeria, E. coli and Salmonella. The company expects to more than double its staff of 12 next year, to support sales and marketing.

Pascal told MedCity News earlier this year that its diagnostic platform could be used to detect hospital acquired infections. Such a move would require securing 510(k) approval from the U.S. Food and Drug Administration, but Pascal said the design of its diagnostic platform means that when the company is ready to shift its attention to HAI, it could make such a submission in a relatively short timeframe.

Detecting Biothreats, Faster and Cheaper

Scientists at the Texas Biomedical Research Institute (TBRI) have created a fast and efficient way of developing tests for potential bioterror agents. The technique, published on November 5, 2012 in Scientific Reports, quickly identifies antibodies that recognize bacterial toxins or viral proteins in a few days, using simple equipment found in most facilities around the world.

This technique is “more suitable for resource limited laboratories” than traditional methods that require expensive equipment like chromatography systems,  said Kim Janda, a chemist from the Scripps Research Institute, who was not involved in the study. “I think it will find ample use in other laboratories in the future.” 

Currently, to find antibodies that recognize potential biological threats—a key step towards developing effective diagnostics—scientists start with a large panel of possible antibodies, and gradually isolate those that recognize a given target. It is a laborious process—each round of screening can identify hundreds of antibodies, which have to be individually purified using large cultures and expensive equipment like chromatography systems. The whole process can take months.

“I was faced with this dilemma of deconvoluting hundreds of antibodies, and didn’t want to spend a year purifying the darn things,” said TBRI’s Andrew Hayhurst , who studies ways to detect biothreats.

So, together with TBRI colleague Laura Sherwood, he devised a solution. He starts by making extracts from different strains of E. coli, each engineered to produce a slightly different antibody. Each extract is loaded into a separate well on a large plate. The antibodies all have a molecule called biotin on their tail, which binds tightly to neutravidin, a protein that coats the wells.

Then, Hayhurst adds the target. It sticks to some of the immobilized antibodies, but not others. He adds another round of antibodies that bind to the immobilized targets. Finally, he applies another batch of neutravidin that sticks to the second layer of antibodies, this time labeled with a tag that can be made visible to the naked eye, such as a fluorescence marker. He rinses the plate to remove any loose tags, and simply looks for which wells are producing the right color, indicating the antibodies in that well successfully recognized the microbial target. 

Hayhurst and Sherwood used their method to identify pairs of antibodies against two potential bioterror weapons - botulinum toxin, one of the most potent known bacterial poisons, and Ebola virus. By rapidly finding antibodies that bind to such target, scientists could quickly develop tests for them. “It’s an environmental surveillance tool,” said Hayhurst.

The same method could also be used to develop new diagnostic tests for “virtually any target,” Hayhurst said. For the moment, he is focusing on known biothreats, but the technique could eventually be help create a rapid response to an unfamiliar threat used in an attack, he said. “The knowledge gained in targeting the known will be of use in smoothing the path to targeting the unknown.”

The system is incredibly simple, and takes very little equipment. All the E. coli strains can be grown in milliliter-sized table-top cultures. “Anyone in the world can just do this on their bench,” said Hayhurst. “It’s so simple, there’s no witchcraft involved. It’s about the cheapest way of doing this possible.”

When the cultures are ready, it takes just an hour to screen hundreds of antibodies at once. The technique immediately focuses an experimenter’s attention on the effective antibodies, bypassing the need to purify them. And once the right antibodies have been identified, Hayhurst can produce them en masse using the same engineered E. coli strains. “You can immediately start cranking out milligrams of antibodies,” he said.

“I am extremely excited by these innovations,” said Paul Gulig, a microbiologist from the University of Florida who was not involved in the study. “They streamlined many things.”

L. J. Sherwood & A. Hayhurst., “Hapten mediated display and pairing of recombinant antibodies accelerates assay assembly for biothreat countermeasures,” Scientific Reports, doi:10.1038/srep00807, 2012.


Veredus Introduces the Vere MTB Chip for Fast Diagnosis of TB

Tuberculosis (TB) is a common, and in many cases lethal infectious diseases caused by various strains of mycobacterium, usually Mycobacterium tuberculosis complex. It is spread through the air when people who have an active MTB infection cough, sneeze, or otherwise transmit their saliva through the air. Most infections in humans result in an asymptomatic, latent infection, and about one in ten latent infections eventually progress to active disease, which, if left untreated, kills more than 50% of those infected.

Global prospects for TB control are challenged by the emergence of drug-resistant strains, especially those that are multidrug resistant (MDR) and extensively drug resistant (XDR). Soon after anti-TB drugs became available in the 1940s came reports of drug resistance among patients undergoing treatment. The prevalence of TB resistance to a single drug was continuously on the rise in several parts of the world, and eventually in the early 1990s, multiple converging factors led to an explosive emergence of MDR-TB, defined as resistance to the two most effective first-line anti-TB agents, Isoniazid and Rifampicin. In 2010, there were an estimated 650 000 cases of MDR-TB.

The threat of tuberculosis has propelled the need of a new tuberculosis diagnostic test system that should be able to do fast and reliable detection and identification of Mycobacterium tuberculosis complex, with the capability to differentiate it from clinically relevant non-tuberculous mycobacterium species as well as detecting drug resistance especially multidrug resistance.

Singapore based Veredus Laboratories announced the launch of its VereMTB™ multiplexed lab-on-a-chip for the detection of various mutations of mycobacterium responsible for causing tuberculosis as well as nine other similar clinically interesting mycobacterium. The chip identifies the specific mycobacterium within three hours after being presented with a sample of coughed up direct sputum.

The technology doesn’t require culturing the bacteria, a slow process that can extend into days when rapid detection is key. The VereMTB is a nucleic acid-based, Lab-On-Chip (LOC) device which combines multiplex PCR and microarray hybridization assay to detect, differentiate and identify:10 different mycobacterium strains with special emphasis on Mycobacterium tuberculosis Complex (MTBC) and its Resistance to Rifampicin and/or Isoniazid from Pulmonary Clinical Specimens or Cultivated Samples (MDR-TB).

Based on STMicroelectronics’ technology, the VereMTB chip is currently undergoing evaluations by the Chinese Center for Disease Control and Prevention in Beijing, China as part of their ongoing program to assess new technologies for TB diagnostics. According to the 2012 World Health Organization report on TB, India and China combined have almost 40 percent of the world’s TB cases, and nearly 60% of multi-drug resistant cases in 2011 were in India, China, and the Russian Federation.

“At the main CDC National TB Reference Lab in Beijing, we have been evaluating VereMTB using samples, collected from across China with a special interest in detecting challenging multi-drug resistant strains that are difficult to detect using other methods,” said Professor Zhao Yanlin Director of National TB Reference Laboratory and Vice Director of the National Center for Tuberculosis Control and Prevention at the Chinese Center for Disease Control and Prevention. “The speed, accuracy and comprehensiveness of the results have been very promising. We look forward to continuing our collaboration with Veredus for new breakthroughs in diagnosing TB.”