Rapid No-Spin Chlamydia RNA Extraction via Filtering, Lysis and Monolith Binding

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DESCRIPTION (provided by applicant): This application addresses the urgent need for expanded screening and test-and-treat programs for Chlamydia trachomatis (CT) through the development of a fast, straightforward sample preparation method. CT infection, which is often asymptomatic in female patients, can result in pelvic inflammatory disease and irreversible infertility in the infected individual as well as blindness in infants born to infected mothers. CT infection can be readily resolved through a short course of antibiotics, but achieving optimal patient outcomes depends on identifying infection and prescribing treatment within a single visit to a doctor's office, hospital, or clinic-the "test-and-treat" approach to infectious disease care. Multiple studies have shown current rapid CT antigen tests to exhibit such poor sensitivity as to have almost no value in clinical decision making. In contrast, both the sensitivity and the specificity of nucleic acid testing for CT infection typically exceed 95%. With increasing availability and low cost of compact thermocyclers and other emerging nucleic acid testing technologies, smaller clinics are increasingly well positioned to run the amplification and detection steps in CT nucleic acid testing. Yet the requisite preparation of vaginal swab and urine samples for subsequent CT nucleic acid testing-including lysis, filtering, and extraction and elution of bacterial RNA and DNA-is a barrier to widespread adoption of CT nucleic acid testing outside of sophisticated laboratories. This application seeks to enable expanded access to CT nucleic acid testing through the development of high- performance, fully automated CT sample preparation in an inexpensive, disposable cartridge. The usage procedure consists of simply placing a urine or vaginal swab sample in a small cup, which attaches to the cartridge. Slit capillary array fluidic actuator (SCAFA) chips-an innovative technology recently developed by the Applicant Organization-are built into the disposable cartridge and drive all sample and reagent transport steps entailed in a high-extraction-efficiency sample preparation process. The extraction process will leverage an innovative, fully cartridge-integrated (no centrifugation) soli phase extraction method using porous polymer monoliths within short glass capillaries, tuned to have optimal porosity for efficient capture of a nucleic acid target without clogging. The sample preparation process executed within the cartridge also includes pre- extraction steps of sample metering, filtering CT from sample, lysing CT on the filter, and elution from the filter. Sample-in to results-out turnaround time is 45 minutes. This Phase I project is organized around two specific aims. Specific Aim 1 focuses on the sample prep module's front end, including metering and lysing. Specific Aim 2 focuses on high-yield extraction in the porous polymer monolith, including monolith composition and capture/elution chemistry. The two Aims collectively establish the feasibility of the high-performance, low-cost CT sample preparation cartridge, laying groundwork for full development in Phase II.