Predicting Antimicrobial MICs for Nontyphoidal Salmonella Using Multitask Representations Learning

Teng Lin

Abstract: The antimicrobial resistance (AMR) pathogens have become an increasingly worldwide issue, posing a significant threat to global public health. To obtain an optimized therapeutic effect, the antibiotic sensitivity is usually evaluated in a clinical setting, whereas traditional culture-dependent antimicrobial sensitivity tests are labor-intensive and relatively slow. Rapid methods can greatly optimize antimicrobial therapeutic strategies and improve patient outcomes by reducing the time it takes to test antibiotic sensitivity. The booming development of sequencing technology and machine learning techniques provide promising alternative approaches for antimicrobial resistance prediction based on sequencing. In this study, we used a lightweight Multitask Learning Transformer to predict the MIC of 14 antibiotics for Salmonella strains based on the genomic information, including point mutations, pan-genome structure, and the profile of antibiotic resistance genes from 5,278 publicly available whole genomes of nontyphoidal Salmonella. And we got better prediction results (improved more than 10% for raw accuracy and 3% for accuracy within ±1 2-fold dilution step) and provided better interpretability than the other ML models. Besides the potential clinical application, our models would cast light on mechanistic understanding of key genetic regions influencing AMR.

Anonymous Url: I certify that there is no URL (e.g., github page) that could be used to find authors’ identity.

No Acknowledgement Section: I certify that there is no acknowledgement section in this submission for double blind review.

Code Of Ethics: I acknowledge that I and all co-authors of this work have read and commit to adhering to the ICLR Code of Ethics

Submission Guidelines: Yes

Please Choose The Closest Area That Your Submission Falls Into: Machine Learning for Sciences (eg biology, physics, health sciences, social sciences, climate/sustainability )