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bioRxiv · 10.1101/2021.06.26.450028

Prediction of antibiotic resistant strains of bacteria from their beta-lactamases protein

Maryam, L.·Dhall, A.·Patiyal, S.·Usmani, S. S.·Sharma, N.·Raghava, G. P. S.
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Abstract

Number of beta-lactamase variants have ability to deactivate ceftazidime antibiotic, which is the most commonly used antibiotic for treating infection by Gram-negative bacteria. In this study an attempt has been made to develop a method that can predict ceftazidime resistant strains of bacteria from amino acid sequence of beta-lactamases. We obtained beta-lactamases proteins from the {beta}-lactamase database, corresponding to 87 ceftazidime-sensitive and 112 ceftazidime-resistant bacterial strains. All models developed in this study were trained, tested, and evaluated on a dataset of 199 beta-lactamases proteins. We generate 9149 features for beta-lactamases using Pfeature and select relevant features using different algorithms in scikit-learn package. A wide range of machine learning techniques (like KNN, DT, RF, GNB, LR, SVC, XGB) has been used to develop prediction models. Our random forest-based model achieved maximum performance with AUROC of 0.80 on training dataset and 0.79 on the validation dataset. The study also revealed that ceftazidime-resistant beta-lactamases have amino acids with non-polar side chains in abundance. In contrast, ceftazidime-sensitive beta-lactamases have amino acids with polar side chains and charged entities in abundance. Finally, we developed a webserver "ABCRpred", for the scientific community working in the era of antibiotic resistance to predict the antibiotic resistance/susceptibility of beta-lactamase protein sequences. The server is freely available at (http://webs.iiitd.edu.in/raghava/abcrpred/). Key PointsO_LICeftazidime is commonly used to treat infection caused by Gram-negative bacteria. C_LIO_LIBeta-lactamase is responsible for lysing ceftazidime, make it resistant to bacteria. C_LIO_LIComparison of resistant and sensitive variants of beta-lactamase. C_LIO_LIClassification of sensitive and resistant strain of bacteria based on beta-lactamase. C_LIO_LIPrediction models have been developed using different machine learning techniques. C_LI

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Maryam, L., Dhall, A., Patiyal, S., Usmani, S. S., Sharma, N., Raghava, G. P. S.. 2021-06-27. Prediction of antibiotic resistant strains of bacteria from their beta-lactamases protein. https://doi.org/10.1101/2021.06.26.450028

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