The Rapid Micro Blog

Our blog will keep you informed of new and noteworthy technologies, reviews of recent publications and presentations, upcoming conferences and training events, and what's changing in the rapid and alternative microbiological methods world.

New Pathogen Tests Put Focus on Speed

When a patient is ill with an unknown infection, time is of the essence. But detecting the root cause and determining the best treatment can often take a day or more. Now, start-up companies and laboratories are developing new approaches to determine rapidly which bacteria, virus, or fungus a patient is fighting, with applications that extend well beyond hospital walls. Initial efforts are focused on the health care setting where a doctor needs to know what drug to give, but potential uses include monitoring the safety of the food supply and the environment.

John McDonough is chief executive of T2 Biosystems, a Lexington start-up that devised a prototype of a technology capable of detecting in about two hours a fungal pathogen called Candida, which can cause a serious bloodstream infection. He ticked off a range of potential applications for the technology, which can be tailored to detect other pathogens: “Food samples, contaminated water supplies, manufacturing lines that need to be tested.’’

In the fall, the company presented the results of an analysis of patient samples using the new technology, and its results matched those found using an older technology that takes several days to make the identification. Later this year, his company plans to begin a clinical trial of the new technology.

Detection methods being pioneered vary. One depends on telltale flashes of light, one detects patterns generated when minuscule, magnetic particles bind to a pathogen, and another analyzes DNA to distinguish what microbe is the culprit.

Pathogenica, a Cambridge start-up, is utilizing powerful genome sequencing technologies to identify the type of microbe in a sample.

Hatice Altug, assistant professor of electrical and computer engineering at Boston University, designs chips with many tiny apertures in a gold film - holes that are so small each one is less than 1 percent of the width of a human hair. The holes transmit light whose color changes when a particular virus binds to a hole.

Meanwhile, researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University have been creating technology capable of rapid pathogen identification that works by pulling pathogens from a sample, allowing detection and identification of even very small populations of bacteria, fungi, viruses, or parasites.

This fall, the Wyss received a $12.3 million grant from the Defense Advanced Research Projects Agency to take the technology initially developed to identify pathogens to the next level.

Instead of simply pulling pathogens out of the blood to figure out what type of an infection it is, researchers will work on developing a method to clear pathogens from the blood altogether.

It is not clear which of the many potential approaches will work best, or in what settings each will be most useful. Researchers and companies need to be able to detect tiny amounts of microbes - down to just a few cells in a vial of blood. They also want to develop techniques that take no more than a few hours while keeping costs down.

Altug, for example, is building a single chip capable of detecting many kinds of viruses. Her hope is that the technology could be deployed cheaply in places where it is needed, such as developing countries or in the field. She is also developing a way to analyze the chip using a cellphone camera, instead of expensive lab equipment.

At Pathogenica, scientists are developing a way to use cutting-edge genome sequencing technology to identify a pathogen, its susceptibility to different drugs, and its virulence. The technique takes longer than some in the pipeline, but it can glean a broad array of information.

“You’re looking at the DNA, you can test for multiple pathogens at once; you can have a test that looks for a dozen bacteria at once and that gives you more flexibility,’’ said Alex Rolfe, who is Pathogenica’s director of bioinformatics.

“Instead of just detecting the bacteria, you can test for [drug] resistance at the same time,’’ he said, or detect the difference, say, between the type of E. coli bacteria that normally live in intestines and those that produce toxic molecules.

T2 Biosystems takes advantage of a technology more commonly used in medical scans - the familiar MRI.

The company has developed minuscule magnetic particles that selectively bind to specific pathogens, producing different patterns when exposed to a magnetic field, depending on whether they have latched on to a particular pathogen.

Overall, each technology is still in development and has yet to displace older methods that may require more specialized equipment or days of waiting, but the need is clear.

“If it takes more than two hours, maybe three at the most, it’s too late - they put them [patients] on the drug that quickly, and they won’t change them off that drug, unless they absolutely know they’ve got the right drug,’’ Ingber said. “You want to get in as early as you can.’’

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