This work presents the rapid and portable detection of azole-resistant Aspergillus fumigatus on clinical and environmental isolates collected from around the world using a lab-on-a-chip diagnostic system based on semiconductor technology.. Rapid detection of azole-resistant Aspergillus fumigatus in clinical and 3 environmental isolates using lab-on-a-chip diagnostic system

Aspergillus fumigatus has widely evolved resistance to the most commonly used class of antifungal chemicals, the azoles. Current methods for identifying azole resistance are time-consuming and depend on specialized laboratories. There is an urgent requirement for rapid detection of these emerging pathogens at point-of-need to inform treatment in the clinic. There is a further need for management of environmental reservoirs to enable mitigation of the amplification of antifungal resistance. Our study demonstrates the rapid and portable detection of the two most relevant genetic markers linked to azole resistance, the mutations TR34 and TR46, found in the promoter region of the gene encoding the azole drug-target, cyp51A. This detection is developed using a conventional lab-based instrument and then translated to our lab-on-a-chip platform comprised of: (1) tandem-repeat loop-mediated isothermal amplification; (2) state-of-the-art complementary metal-oxide-semiconductor microchip technology; (3) and a smartphone application for data acquisition, visualization and cloud connectivity. Experiments were performed using isolates from clinical and environmental samples from 6 countries across 5 continents, showing a lower limit-of-detection of 10 genomic copies per reaction in less than 30 minutes. When fully integrated with a sample preparation module, this diagnostic system will enable the detection of this ubiquitous fungus at the point-of-need, improving clinical decision making, infection control and epidemiological surveillance.