Journal:Hierarchical AI enables global interpretation of culture plates in the era of digital microbiology
| Full article title | Hierarchical AI enables global interpretation of culture plates in the era of digital microbiology |
|---|---|
| Journal | Nature Communications |
| Author(s) | Signoroni, Alberto; Ferrari, Alessandro; Lombardi, Stefano; Savardi, Mattia; Fontana, Stefania; Culbreath, Karissa |
| Author affiliation(s) | University of Brescia, Copan WASP, Tricore Laboratories |
| Primary contact | Email: alberto dot signoroni at unibs dot it |
| Year published | 2023 |
| Volume and issue | 14 |
| Article # | 6874 |
| DOI | 10.1038/s41467-023-42563-1 |
| ISSN | 2041-1723 |
| Distribution license | Creative Commons Attribution 4.0 International |
| Website | https://www.nature.com/articles/s41467-023-42563-1 |
| Download | https://www.nature.com/articles/s41467-023-42563-1.pdf (PDF) |
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Abstract
Full laboratory automation is revolutionizing work habits in an increasing number of clinical microbiology facilities worldwide, generating huge streams of digital images for interpretation. Contextually, deep learning (DL) architectures are leading to paradigm shifts in the way computers can assist with difficult visual interpretation tasks in several domains. At the crossroads of these epochal trends, we present a system able to tackle a core task in clinical microbiology, namely the global interpretation of diagnostic bacterial culture plates, including presumptive pathogen identification. This is achieved by decomposing the problem into a hierarchy of complex subtasks and addressing them with a multi-network architecture we call DeepColony. Working on a large stream of clinical data and a complete set of 32 pathogens, the proposed system is capable of effectively assisting plate interpretation with a surprising degree of accuracy in the widespread and demanding framework of urinary tract infections (UTIs). Moreover, thanks to the rich species-related generated information, DeepColony can be used for developing trustworthy clinical decision support services in laboratory automation ecosystems from local to global scale.
Keywords: bacteriology, clinical microbiology, computer science, urinary tract infection, laboratory automation, deep learning
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