The Great ESKAPEE: Multi-Omic Methods for Bacterial Profiling Using HILIC-IM-MS

The prominence of antibiotic resistant bacterial strains has raised concern for the efficacy of currently available antibiotics. Point-of-care utilization of existing drug therapies require strain specific identification of pathogens, which often demands tedious sample preparation strategies and tailored analytical methods. The emergence of multi-omics approaches has empowered scientists to answer complex systems biology questions regarding antibiotic resistance. The Centers for Disease Control disclosed in a 2019 report, identifying some of the most prominent multi-drug resistant bacteria, E.S.K.A.P.E.E. pathogens, that contribute to infection that may lead to high rates of mortality and increased economic strain from health-care associated costs. The genomic and proteomic information of these antibiotic resistant pathogens, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli have been thoroughly explored. However, there remains a significant lack of knowledge of the downstream metabolomic and lipidomic profiles of these small organisms. Here, we have optimized a high throughput multiomics approach that can isolate the constituent parts of the whole biological system that are not otherwise explained by the template-driven aspects of genomics and proteomics. We showcase the potential for a streamlined method for managing multi-omics experiments of diverse antibiotic resistant microbe populations using an optimized workflow.¹ 

(1) Carpenter, J. M.; Hynds, H. M.; Bimpeh, K.; Hines, K. M. ACS Measurement Science Au 2023.