Rapid Identification of Bacterial isolates Using Microfluidic Adaptive Channels and Multiplexed Fluorescence Microscopy

16 July 2023


Stelios Chatzimichail, Piers Turner, Conor Feehily, Alison Farrar, Derrick Crook, Monique Andersson, Sarah Oakley, Lucinda Barrett, Hafez El Sayyed, Jingwen Kyropoulos, Christoffer Nellåker, Nicole Stoesser, Achillefs N. Kapanidis medRxiv 2023.07.16.23292615; doi: https://doi.org/10.1101/2023.07.16.23292615

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We demonstrate the rapid capture, enrichment, and identification of bacterial pathogens using Adaptive Channel Bacterial Capture (ACBC) devices. Using controlled tuning of device backpressure in polydimethylsiloxane (PDMS) devices, we enable the controlled formation of capture regions capable of trapping bacteria from low cell density samples with near 100% capture efficiency. The technical demands to prepare such devices are much lower compared to conventional methods for bacterial trapping and can be achieved with simple benchtop fabrication methods. We demonstrate the capture and identification of seven species of bacteria with bacterial concentrations lower than 1000 cells/mL, including common Gram-negative and Gram-positive pathogens such as Escherichia coli and Staphylococcus aureus. We further demonstrate that species identification of the trapped bacteria can be undertaken in the order of one-hour using multiplexed 16S rRNA-FISH with identification accuracies of 73-99% with unsupervised classification methods.