The discovery of antibiotics has been slowing to a halt. Phenotypic screening is once again at the forefront of antibiotic discovery, yet Mechanism-Of-Action (MOA) identification is still a major bottleneck. As such, methods capable of MOA elucidation coupled with the high-throughput screening of whole cells are required now more than ever, for which Fourier-Transform Infrared (FTIR) spectroscopy is a promising metabolic fingerprinting technique. A high-throughput whole-cell FTIR spectroscopy-based bioassay was developed to reveal the metabolic fingerprint induced by 15 antibiotics on the Escherichia coli metabolism. Cells were briefly exposed to four times the minimum inhibitory concentration and spectra were quickly acquired in the high-throughput mode. After preprocessing optimization, a partial least squares discriminant analysis and principal component analysis were conducted. The metabolic fingerprints obtained with FTIR spectroscopy were sufficiently specific to allow a clear distinction between different antibiotics, across three independent cultures, with either analysis algorithm. These fingerprints were coherent with the known MOA of all the antibiotics tested, which include examples that target the protein, DNA, RNA, and cell wall biosynthesis. Because FTIR spectroscopy acquires a holistic fingerprint of the effect of antibiotics on the cellular metabolism, it holds great potential to be used for high-throughput screening in antibiotic discovery and possibly towards a better understanding of the MOA of current antibiotics.Metabolites 2020, 10, 145 2 of 15 of finding compounds with unique biological and/or chemical properties and limited insight in the pharmacological target. Additionally, phenotypic screening does not explore the chemical grey matter, i.e., compounds capable of inducing some level of phenotypic modulation, but without sufficient potency to induce cell death or growth inhibition, which can be a source of compounds suitable for lead optimization with medicinal chemistry techniques [5,6]. Antibiotic discovery is a very challenging task, but identifying the MOA has proven equally challenging [7]. Currently, determining the MOA of antibiotics is still a bottleneck of the phenotypic screening discovery process, for which metabolomics holds great potential. As such, the ability to rapidly infer MOA and, if possible, the biomolecular target of antibiotics is increasingly important given the pressing need for new antibiotics. Currently, screening hundreds of thousands of compounds is a reasonable throughput of a drug discovery program, in part due to the ease in synthetizing bioactive compounds, and in part given the increasing availability of natural product libraries [8]. Two concepts are relevant when discussing MOA identification. One is determining the molecular pathways affected by a given compound:the drug effects. The second is the specific compound-substrate interactions:the drug target [9]. Although both concepts are very important in antibiotic discovery, given the exploratory purpo...