Rapid, automated, and reliable antimicrobial susceptibility test from positive blood culture by CAST‐R

• Published in: mLife Vol. 1; no. 3; pp. 329 - 340
• Main Authors: Zhu, Pengfei, Ren, Lihui, Zhu, Ying, Dai, Jing, Liu, Huijie, Mao, Yuli, Li, Yuandong, He, Yuehui, Zheng, Xiaoshan, Chen, Rongze, Fu, Xiaoting, Zhang, Lili, Sun, Lijun, Zhu, Yuanqi, Ji, Yuetong, Ma, Bo, Xu, Yingchun, Xu, Jian, Yang, Qiwen
• Format: Journal Article
• Language: English
• Published: Australia John Wiley & Sons, Inc 01.09.2022; John Wiley and Sons Inc; Wiley
• Subjects: Antimicrobial agents; antimicrobial susceptibility test; Automation; Datasets; Infections; laboratory automation; Metabolism; Metabolites; Method; Methods; Mortality; Pathogens; Performance evaluation; Raman; Sepsis; tigecycline; Raman; laboratory automation; antimicrobial susceptibility test; tigecycline; sepsis
• ISSN: 2770-100X; 2097-1699; 2770-100X
• DOI: 10.1002/mlf2.12019

Antimicrobial susceptibility tests (ASTs) are pivotal in combating multidrug resistant pathogens, yet they can be time‐consuming, labor‐intensive, and unstable. Using the AST of tigecycline for sepsis as the main model, here we establish an automated system of Clinical Antimicrobials Susceptibility Test Ramanometry (CAST‐R), based on D2O‐probed Raman microspectroscopy. Featuring a liquid robot for sample pretreatment and a machine learning‐based control scheme for data acquisition and quality control, the 3‐h, automated CAST‐R process accelerates AST by >10‐fold, processes 96 paralleled antibiotic‐exposure reactions, and produces high‐quality Raman spectra. The Expedited Minimal Inhibitory Concentration via Metabolic Activity is proposed as a quantitative and broadly applicable parameter for metabolism‐based AST, which shows 99% essential agreement and 93% categorical agreement with the broth microdilution method (BMD) when tested on 100 Acinetobacter baumannii isolates. Further tests on 26 clinically positive blood samples for eight antimicrobials, including tigecycline, meropenem, ceftazidime, ampicillin/sulbactam, oxacillin, clindamycin, vancomycin, and levofloxacin reveal 93% categorical agreement with BMD‐based results. The automation, speed, reliability, and general applicability of CAST‐R suggest its potential utility for guiding the clinical administration of antimicrobials. Impact statement Rapid and reliable antimicrobial susceptibility tests (ASTs) are pivotal to effective, safe, and environmentally responsible treatment of acute infections such as sepsis. For example, conventional ASTs for tigecycline, a last‐resort antimicrobial treating blood infections, have been slow, tedious, and even plagued by inaccuracy, due to the drug's sensitivity to the dissolved oxygen in broth. Here employing tigecycline as the main model, we establish an automated system of Clinical Antimicrobials Susceptibility Test Ramanometry (CAST‐R), based on D2O‐probed Raman microspectroscopy. Results from Acinetobacter baumannii isolates as well as clinically positive blood samples show that the 3‐h CAST‐R process achieves excellent accuracy yet accelerates AST by >10‐fold.