ABERDEEN PROVING GROUND, Md. — U.S. Army civilian microbiologists are using an offline bioinformatics tool that collects gigabytes of data and distills it into actionable results.
Army civilian microbiologists from the Chemical, Biological, Radiological, Nuclear, Explosives Analytical and Remediation Activity, or CARA, are working with the Army Chemical Biological Center to leverage the MinION Detection Software, or MINDS, an offline bioinformatics tool that interfaces between genomic information and maps it to a library.
Based on Aberdeen Proving Ground, Maryland, CARA is part of the 20th CBRNE Command, the U.S. military’s premier all hazards command. CARA is an all Army civilian organization that conducts mobile laboratory operations, emergency response missions for Recovered Chemical Warfare Material and technical escort of surety and non-surety chemical material.
With mobile expeditionary laboratories, CARA provides theater-level validation of chemical and biological warfare agents, toxic industrial chemicals and explosives to support operations. These distinct laboratory capabilities are designated to support the combatant commanders or joint task force commanders when called upon to deploy into their area of operations.
Dr. Timothy M. Reed, an Army microbiologist at CARA, said the bioinformatics tool increases the ability of CARA’s expeditionary laboratories to produce biological threat information.
“Until recently, CARA’s biological detection capabilities were limited to those organisms that we had targeted methods for,” said Reed. “We could only detect a few dozen of biological targets of interest. Unfortunately, this did not allow us to confirm identification of any organism that was outside our detection methods.”
According to Reed, this testing method was similar to a patient visiting a doctor with a sore throat and fever and only being tested for flu, strep and COVID-19.
“If all tests come back negative, no further identification can be made for the causal agent of the illness and the patient is left not knowing what is wrong with him or what possible disease he has,” said Reed, a Dallas native who has served at CARA since 2014. “If a sample was outside our detection capabilities, we would have a difficult time trying to identify it.”
Reed said the development of nanopore technology has given CARA the capability to sequence everything in a sample and identify unknowns using entire libraries of microorganisms that contains hundreds of thousands of different organisms and species.
In collaboration with the Chemical Biological Center, Dr. Samir Deshpande developed MINDS to provide the same data analysis available in an online cloud-based software to a stand-alone, offline software package.
With this application, the graphical user interface developed by Deshpande runs Centrifuge, a freely available classification software developed by Johns Hopkins University, which identifies all the organisms in a sample by mapping them to a reference library.
“With MINDS, CARA has all the capabilities of a cloud-based online software now contained in a portable offline laptop that enables CARA to utilize the MinION field sequencer anywhere and not require connection to the internet,” said Reed.
Reed said CARA has used MINDS during several recent field exercises, including exercises at Fort Bliss, Texas, and Dugway Proving Ground, Utah, where samples were received and analyzed through MINDS offering orthogonal confirmation to other analytical instrumentation. During the most recent exercise on Fort Bliss, the sequencing technology was able to identify an unknown sample that other devices were not able to detect.
CARA first used MINDS in 2018 at a laboratory in the U.S. Central Command area of operations. Reed said the U.S. Navy, Centers for Disease Control and Food and Drug Administration are also working to incorporate the same detection technology.
“With each exercise, the MinION sequencing technology, along with MINDS bioinformatics tool, matures and demonstrates the need and usefulness of a technology that is not constrained with two dozen detection targets,” said Reed.
“MinION sequencing technology, along with the MINDS platform, provide biological threat intelligence at higher confidence to the combatant commanders,” said Reed. “Once the biological threat has been confidently described, commanders can take appropriate countermeasures.”
Franz Amann, the director of CARA, said Army civilians at his activity lean forward on leveraging technology to better accomplish their high stakes missions.
“Our CARA microbiologists leading the way to incorporate this detection capability into their laboratory operations to provide better support to the warfighter,” said Amann, a retired Chemical Corps officer from Spartanburg, South Carolina. “Army civilians at CARA are always looking for better ways to defend our nation and support the warfighters who defend it.
“Expanding our microbiological capabilities allows our team to test and validate a wider spectrum of potential biological agents in theater,” said Amann. “This theater-validation capability allows our team to advise the combatant and joint task force commander so they can make timely decisions. Sending samples back to the states or another approved nation to test is time consuming, which causes delays in the critical decision-making process.”