Rapid Microbial Identification and Characterization in the Field

Antimicrobial resistance (AMR) in pathogens is a critical issue in the United States, with >2.8 million antibiotic-resistant infections occurring each year and >35,000 people dying as a result. Wounded warfighters in the field are particularly vulnerable to the dangers of resistant pathogens. Supporting wound healing by gaining an understanding of resistance mechanisms of microbial pathogens would provide a significant new capability for expeditionary medicine in austere environments and is a crucial gap identified by the Surgeon General of the Air Force. Improving diagnosis and characterization of resistant bacteria has also been identified as a national strategic goal. Currently, determining whether a pathogen is resistant to antibiotics requires days or weeks of culturing and susceptibility testing. Even rapid clinical microbiology tests take 36-48 hours to run. However, AMR is conferred by changes in the microbial genome, and the initial phase of this project demonstrated that highly accurate prediction of AMR phenotypes is possible using only genome sequencing data. Unlike standard sequence analysis pipelines that require significant bioinformatics expertise, these capabilities are made available via a graphical user interface as plugins to Parabon’s existing Fx™ DNA Analysis Platform. Fx’s deployment is highly flexible and can run remotely, on a local server, or even on a single machine, making it adaptable for forward-deployment use cases. Originally designed for forensic analysis of human DNA, Fx provides a user-friendly interface for any type of complex sequence analyses. The next phase of this project will enhance these software tools to produce a deployable solution for detecting and characterizing pathogens in the field.