Contamination Source Identification (CSI), a company working out of the Juniata College Center for Entrepreneurial Leadership (JCEL) in Huntingdon is set to revolutionize the way infectious diseases are diagnosed.
The company is finalizing a protocol which will allow for significantly faster and more comprehensive diagnosis of infectious diseases using a combination of a wet lab robot (the Biomek i7 Automated Workstation) to process samples, a DNA sequencer and a supercomputer.
“I really do think this is going to be big,” said Dr. Regina Lamendella, co-owner of CSI and Velco Professor of Biological Science at Juniata College. “We’re hoping that this diagnostic test will revolutionize the current infectious disease market. We think it’s going to change the way diagnostics are done because of how quickly we can do it, less than 24 hours, and how comprehensive it is. So it’s not like we’re just looking at one type of bacteria at a time, we’re looking at everything.”
Current methods have their downsides.
“The current way these tests are done is through classical micro-biology techniques. You might remember when you had strep throat, you’d have a doctor swabbing your throat and swabbing that onto a petri dish and growing that culture overnight. You won’t hear back about the answer for many, many days because you have to grow the organism and takes a lot of time. That, and the rate of false negatives are quite high for the current standard of care,” said Lamendella.
CSI has taken an entirely different approach.
“So the new way to do this, and it’s very cutting edge, is instead of growing the organism and looking at it under the microscope, what we do is sequence the DNA directly from the organism. I liken us to the 23 and Me of bacteria,” she said.
A few comparable services are available, but they are out of most people’s price range.
“Because all of this is very new, and because molecular biology is very expensive, the current labs that are offering similar services are charging thousands and thousands of dollars for one single test,” said Lamendella.
She hopes CSI’s test will be much more affordable, making it accessible to the general population.
Once the wet lab robot pulls out the the samples’ DNA, it is sent to a sequencer which does approximately 400 million sequences at a time.
The sequencer then streams the data to the supercomputer which provides the test report, or diagnosis, that then goes directly to the hospital.
CSI is able to provide a diagnosis in 10 hours, running 96 samples at a time through the automated robot.
Receiving a quick diagnosis would allow for more targeted therapy early on to knock out an infection and stop antibiotic resistance from perpetuating itself, as is common when patients are put on broad spectrum antibiotics while waiting for days to get their diagnosis.
Not only is it faster, but more effective in identifying infectious disease.
“The limit of detection is only a couple of bacterial cells, so it’s very, very sensitive, more sensitive than any other test on the market right now,” said Lamendella.
Justin Wright and Gary Shope, both Juniata College alumni, are co-owners with Lamendella.
“This business takes a sophisticated set of different skills; Justin being the computational expert, and there’s me being the molecular biologist, and then Gary being the business man,” said Lamendella. You need to have expertise in the molecular biology, the micro-biology, even ecology, and also computational biology. All the data that the sequencers generate have to be analyzed. We take these sequences and compare them to these big data bases so you can slap a name onto these organisms and say ‘that’s an E. coli, that’s an salmonella.’”
Wright, who oversees the operation of the supercomputer, explained the use of informatics and its importance in reaching a diagnosis.
“Informatics is the synergy of computational science and biology, and one of the widest applications is genomics, the analysis of DNA sequence. So the wet lab side of things is about accruing those sequences of DNA. The informatics is where you carefully, diligently and quickly assign the correct identification to those sequences. This is where the diagnosis happens. If we didn’t have this we wouldn’t be able to make that diagnosis quickly enough to be clinically relevant,” he said. “As soon as we get the data from the sequencer we want to provide an answer within a few hours, maximum.”
CSI’s supercomputer has the power of approximately 400 computers strung together to do the computations that fast.
The company is anticipating it will receive CLIA certification (Clinical Laboratory Improvement Amendments) in October, at which point it will begin being able to accept samples from hospitals.
In the meantime, they are validating their protocol by working on studies with family practice doctors from Hershey and local areas, looking particularly at diagnosing Lyme disease.
The company is planning for growth.
“I think one of the neat things is we are doing this in Huntingdon, Pennsylvania. Being here in JCEL has been nice for a start up company. We’re looking to grow this. The costs are quite low for rent, which is great, and we’ve hired talented students from Juniata and we’re looking to eventually start hiring employees from Huntingdon proper, as well,” said Lamendella. “So we’re hoping this will become what I’m calling the Meta-genomics capital of the world.”
Nathan can be reached at firstname.lastname@example.org.