Rapid and label-free identification of individual bacterial pathogens exploiting three-dimensional quantitative phase imaging and deep learning

Kim, G.; Ahn, D.; Kang, M.; Jo, Y.; Ryu, D.; Kim, H.; Song, J.; Ryu, J. S.; Choi, G.; Chung, H. J.; Kim, K.; Chung, D. R.; Yoo, I. Y.; Huh, H. J.; Min, H.; Lee, N. Y.; Park, Y.

doi:10.1101/596486

bioRxiv · 10.1101/596486

Rapid and label-free identification of individual bacterial pathogens exploiting three-dimensional quantitative phase imaging and deep learning

Kim, G.·Ahn, D.·Kang, M.·Jo, Y.·Ryu, D.·Kim, H.·Song, J.·Ryu, J. S.·Choi, G.·Chung, H. J.·Kim, K.·Chung, D. R.·Yoo, I. Y.·Huh, H. J.·Min, H.·Lee, N. Y.·Park, Y.

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Abstract

The healthcare industry is in dire need for rapid microbial identification techniques. Microbial infection is a major healthcare issue with significant prevalence and mortality, which can be treated effectively during the early stages using appropriate antibiotics. However, determining the appropriate antibiotics for the treatment of the early stages of infection remains a challenge, mainly due to the lack of rapid microbial identification techniques. Conventional culture-based identification and matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy are the gold standard methods, but the sample amplification process is extremely time-consuming. Here, we propose an identification framework that can be used to measure minute quantities of microbes by incorporating artificial neural networks with three-dimensional quantitative phase imaging. We aimed to accurately identify the species of bacterial bloodstream infection pathogens based on a single colony-forming unit of the bacteria. The successful distinction between a total of 19 species, with the accuracy of 99.9% when ten bacteria were measured, suggests that our framework can serve as an effective advisory tool for clinicians during the initial antibiotic prescription. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/596486v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@786668org.highwire.dtl.DTLVardef@8b4eb4org.highwire.dtl.DTLVardef@1dc2452org.highwire.dtl.DTLVardef@1d4888c_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Kim, G., Ahn, D., Kang, M., Jo, Y., Ryu, D., Kim, H., Song, J., Ryu, J. S., Choi, G., Chung, H. J., Kim, K., Chung, D. R., Yoo, I. Y., Huh, H. J., Min, H., Lee, N. Y., Park, Y.. 2019-04-03. Rapid and label-free identification of individual bacterial pathogens exploiting three-dimensional quantitative phase imaging and deep learning. https://doi.org/10.1101/596486

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