Pioneering Klebsiella Pneumoniae Antibiotic Resistance Prediction With Artificial Intelligence-Clinical Decision Support System–Enhanced Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry: Retrospective Study

Abstract

Background The rising prevalence and swift spread of multidrug-resistant gram-negative bacteria (MDR-GNB), especially Klebsiella pneumoniae (KP), present a critical global health threat highlighted by the World Health Organization, with mortality rates soaring approximately 50% with inappropriate antimicrobial treatment. Objective This study aims to advance a novel strategy to develop an artificial intelligence-clinical decision support system (AI-CDSS) that combines machine learning (ML) with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), aiming to significantly improve the accuracy and speed of diagnosing antibiotic resistance, directly addressing the grave health risks posed by the widespread dissemination of pan drug-resistant gram-negative bacteria across numerous countries. Methods A comprehensive dataset comprising 165,299 bacterial specimens and 11,996 KP isolates was meticulously analyzed using MALDI-TOF MS technology. Advanced ML algorithms were harnessed to sculpt predictive models that ascertain resistance to quintessential antibiotics, particularly levofloxacin and ciprofloxacin, by using the amassed spectral data. Results Our ML models revealed remarkable proficiency in forecasting antibiotic resistance, with the random forest classifier emerging as particularly effective in predicting resistance to both levofloxacin and ciprofloxacin, achieving the highest area under the curve of 0.95. Performance metrics across different models, including accuracy, sensitivity, specificity, positive predictive value, negative predictive value, and F1-score, were detailed, underlining the potential of these algorithms in aiding the development of precision treatment strategies. Conclusions This investigation highlights the synergy between MALDI-TOF MS and ML as a beacon of hope against the escalating threat of antibiotic resistance. The advent of AI-CDSS heralds a new era in clinical diagnostics, promising a future in which rapid and accurate resistance prediction becomes a cornerstone in combating infectious diseases. Through this innovative approach, we answered the challenge posed by KP and other multidrug-resistant pathogens, marking a significant milestone in our journey toward global health security.