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.

Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines

“…For example, Salmonella typhimurium ( Salmonella serotype (ser.) typhimurium ), a Gram-negative bacterium, has been well characterized by proteomic analysis [ 191 ]. In 2006, analysis of the Salmonella proteome (∼300 proteins) was performed using infected RAW 264.7 macrophage cells [ 192 ].…”

Monitoring host–pathogen interactions using chemical proteomics

“…Here, we illustrate popular chemical proteomics techniques and summarise recent advances by this approach in the field of host-pathogen communication. [18][19][20] This review focusses on studies employing chemical probes to elucidate biological processes involved in the interplay of animal hosts with pathogenic bacteria/mycobacteria and how this communication can contribute to virulence. Host interactions with the microbiome, [21][22][23][24][25] viruses, [26][27][28] or protozoans, 29,30 have been reviewed elsewhere.…”