A rapid, automated system for bacteria profiling of intra-abdominal infections

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Project Summary New diagnostic tools capable of rapidly identifying and quantifying bacteria within intra-abdominal infections are needed to help clinicians select appropriate antibiotics during the critical early stages of treatment. Current molecular diagnostics remain costly and require access to significant laboratory infrastructure, making them inappropriate for use in small satellite laboratories within the hospital environment. Here we seek to address this urgent need by developing a simple, inexpensive, and automated microfluidic platform capable of evaluating bacteria directly from intra-abdominal abscess fluids to guide initial treatment of infection. The technology will combine on-chip nucleic acid extraction, rapid quantitative PCR (qPCR), and high resolution melt analysis (HRMA) for multiplexed pathogen identification and quantification in under 10 min. The platform will consist of disposable thermoplastic microwell chips and a compact USB-powered reader containing all components for assay operation. Significantly, the entire assay will require only two pipette strokes to discretize sample within a dense array of microliter reaction wells containing all primers and other reagents needed for assay execution. The integration of multiplexed PCR primers into the thermoplastic microwell array during chip manufacture will enable automated thermally-controlled release during PCR, while passive sample discretization within the disposable microwell arrays will further simplify assay operation. Assay times below 10 min will be enabled by integrated thin film electrodes and a unique thermoplastic fabrication technique supporting optimal thermal transport. A disposable piezoelectric element integrated into the chip inlet tube will enable efficient release of nucleic acids prior to sample discretization, and the assay will be operated through an embedded mixed-signal processor supporting all functions, with power and communication provided through a single USB connection to a laptop computer. Using this system, multiplexed qPCR for bacteria identification plus HRMA for product validation will be demonstrated, followed by an investigation of qPCR-HRMA based pathogen identification using unique signatures in the 16S rRNA gene, with a theoretical detection limit of 50 CFU/mL. The technology will be validated within a hospital environment through a clinical study with 50 patients for the simultaneous quantification of 8 bacteria commonly found in intra-abdominal infections, conditions where treatment currently relies on subjective visual assessment and empiric treatment, and where rapid near-patient bacterial identification would transform clinical practice.