Rapid rrna-based molecular detection of microbial and fungal species

Overview

Varigen Biosciences has developed a rapid molecular diagnostic platform that detects bacterial and fungal species by targeting ribosomal RNA (rRNA) using loop-mediated isothermal amplification (LAMP). Because bacterial cells contain approximately 15,000 copies of rRNA and fungal cells contain roughly 100,000 copies, this approach enables single-cell detection sensitivity comparable to PCR while operating at a single temperature of 70°C. The complete assay, from sample to answer, takes less than 30 minutes and requires no complex instrumentation, cold chain logistics, or specialized training. Lyophilized reagents are stable at room temperature and cost approximately $5 per test, making the platform well suited for decentralized testing, field deployment, and resource-limited settings.

Technical specifications

Key features:

• LAMP-based amplification at a constant 70°C using a low-cost heater rather than thermal cycling equipment
• Targets conserved rRNA regions, enabling single bacterial or fungal cell detection
• One-step chemical and heat-based cell lysis with no purification steps required
• Lyophilized reagents stable at room temperature for extended shelf life
• Colorimetric readout as the most affordable option, with a fluorescent readout available through a portable, Bluetooth-coupled instrument and smartphone app for automated result interpretation
• Multiplex capability allowing simultaneous detection of multiple pathogens (yeast, bacteria, and fungi) in separate tubes on the same instrument
• Validated against multiple RNA targets including Ebola, influenza A and B, COVID-19, and West Nile virus, as well as rRNA targets for Escherichia coli, Burkholderia glumae, Staphylococcus aureus, Elizabethkingia meningoseptica, and Blastomyces dermatitidis

Benefits for partners:

• Significantly faster turnaround time compared to traditional culture or PCR workflows
• Lower per-test cost and minimal infrastructure requirements reduce barriers to adoption
• No cold chain dependency simplifies storage, shipping, and field use

Technology readiness level

The core LAMP-based molecular diagnostic chemistry has been validated across multiple viral and microbial targets, with assays for E. coli, Burkholderia glumae, S. aureus, Elizabethkingia meningoseptica, and Blastomyces dermatitidis already demonstrated. Future validation efforts will focus on designing LAMP primers for microbial contaminants relevant to injectable and intravenous fluid manufacturing, optimizing sensitivity and specificity to match PCR benchmarks, integrating a one-step sample preparation method into pre-dispensed lyophilized reaction tubes, and conducting blinded replicate testing on injectable samples. A low-cost instrument prototype under $500 is currently in development, alongside a smartphone application that guides users through assay steps and displays automated positive or negative results, eliminating the need for user interpretation.