Surface Enhanced Raman Spectroscopy and Machine Learning for Identification of Beta-Lactam Antibiotics Resistance Gene Fragment in Bacterial Plasmid

Background: The appearance of antibiotic-resistant bacteria represents a critical medical problem with high risk to patient health. Therefore, simple, express, and reliable methods of antibiotic resistance detection should be developed. Results: In this work, we propose a combination of highly sensitive surface-enhanced Raman spectroscopy (SERS) and machine learning (ML) for the detection of characteristic gene fragments responsible for antibiotic resistance appearance and spreading. To make the detection procedure close to the real case, we used bacterial plasmids as starting biological objects, containing or not the characteristic gene fragment (up to 1:10 ratio), encoding beta-lactam antibiotics resistance. The plasmids were subjected to enzymatic digestion and the created fragments were captured by functional SERS substrates without preliminary (bio)samples separation or purification. Based on subsequent SERS measurements, a database was created for the training and validation of ML. Significance: The reliability of the proposed method was tested on control samples and we showed the possibility of express SEPS-ML detection of bacterial plasmids containing a characteristic gene up to the 10-7 concentration of the initial plasmid, despite the complex composition of the biological sample (i.e. the presence of the excess of alternative plasmids or various biomolecules). The proposed approach provides a good alternative to modern methods for monitoring antibiotic-resistant bacteria and is favored by its simplicity, low detection limit, and the possibility of express and unpretentious analysis.