Proteomic Approaches to Unravel Mechanisms of Antibiotic Resistance and Immune Evasion of Bacterial Pathogens

Abstract

The profound effects of and distress caused by the global COVID-19 pandemic highlighted what has been known in the health sciences a long time ago: that bacteria, fungi, viruses, and parasites continue to present a major threat to human health. Infectious diseases remain the leading cause of death worldwide, with antibiotic resistance increasing exponentially due to a lack of new treatments. In addition to this, many pathogens share the common trait of having the ability to modulate, and escape from, the host immune response. The challenge in medical microbiology is to develop and apply new experimental approaches that allow for the identification of both the microbe and its drug susceptibility profile in a time-sensitive manner, as well as to elucidate their molecular mechanisms of survival and immunomodulation. Over the last three decades, proteomics has contributed to a better understanding of the underlying molecular mechanisms responsible for microbial drug resistance and pathogenicity. Proteomics has gained new momentum as a result of recent advances in mass spectrometry. Indeed, mass spectrometry-based biomedical research has been made possible thanks to technological advances in instrumentation capability and the continuous improvement of sample processing and workflows. For example, high-throughput applications such as SWATH or Trapped ion mobility enable the identification of thousands of proteins in a matter of minutes. This type of rapid, in-depth analysis, combined with other advanced, supportive applications such as data processing and artificial intelligence, presents a unique opportunity to translate knowledge-based findings into measurable impacts like new antimicrobial biomarkers and drug targets. In relation to the Research Topic "Proteomic Approaches to Unravel Mechanisms of Resistance and Immune Evasion of Bacterial Pathogens," this review specifically seeks to highlight the synergies between the powerful fields of modern proteomics and microbiology, as well as bridging translational opportunities from biomedical research to clinical practice.

Keywords: PTMs (post-translational modifications); SWATH-MS; antibiotic resistance; host-pathogen interactions; mass spectometry; system biology.

FIGURE 1

(A) Work-flow followed in bottom-up and top-down proteomics. (B) A schematic workflow for prototypical bottom-up proteomics experiments. Protein lysates from infected biological samples, are digested by trypsin and/or LysC, and the resulting proteolytic peptides are analyzed by LC-MS/MS. (C) Applications and main features of different bottom-up proteomics workflows, label-free or label-based SILAC, and tandem mass tag MS methods applied for global proteome profiling. Workflows can be also coupled with affinity purification-based methods to elucidate host-pathogen PPI networks. (D) Workflow for discovery and validation of biomarkers.