Machine Learning Suggests That Small Size Helps Broaden Plasmid Host Range

Abstract

Plasmids mediate gene exchange across taxonomic barriers through conjugation, shaping bacterial evolution for billions of years. While plasmid mobility can be harnessed for genetic engineering and drug-delivery applications, rapid plasmid-mediated spread of resistance genes has rendered most clinical antibiotics useless. To solve this urgent and growing problem, we must understand how plasmids spread across bacterial communities. Here, we applied machine-learning models to identify features that are important for extending the plasmid host range. We assembled an up-to-date dataset of more than thirty thousand bacterial plasmids, separated them into 1125 clusters, and assigned each cluster a distribution possibility score, taking into account the host distribution of each taxonomic rank and the sampling bias of the existing sequencing data. Using this score and an optimized plasmid feature pool, we built a model stack consisting of DecisionTreeRegressor, EvoTreeRegressor, and LGBMRegressor as base models and LinearRegressor as a meta-learner. Our mathematical modeling revealed that sequence brevity is the most important determinant for plasmid spread, followed by P-loop NTPases, mobility factors, and β-lactamases. Ours and other recent results suggest that small plasmids may broaden their range by evading host defenses and using alternative modes of transfer instead of autonomous conjugation.

Keywords

• conjugation
• horizontal gene transfer
• plasmid host range
• small-size plasmid
• antibiotic resistance genes
• clustering