Proteomics in antibiotic resistance and tolerance research: Mapping the resistome and the tolerome of bacterial pathogens

Abstract

Antibiotic resistance, the ability of a microbial pathogen to evade the effects of antibiotics thereby allowing them to grow under elevated drug concentrations, is an alarming health problem worldwide and has attracted the attention of scientists for decades. On the other hand, the clinical importance of persistence and tolerance as alternative mechanisms for pathogens to survive prolonged lethal antibiotic doses has recently become increasingly appreciated. Persisters and high‐tolerance populations are thought to cause the relapse of infectious diseases, and provide opportunities for the pathogens to evolve resistance during the course of antibiotic therapy. Although proteomics and other omics methodology have long been employed to study resistance, its applications in studying persistence and tolerance are still limited. However, due to the growing interest in the topic and recent progress in method developments to study them, there have been some proteomic studies that yield fresh insights into the phenomenon of persistence and tolerance. Combined with the studies on resistance, these collectively guide us to novel molecular targets for the potential drugs for the control of these dangerous pathogens. In this review, we surveyed previous proteomic studies to investigate resistance, persistence, and tolerance mechanisms, and discussed emerging experimental strategies for studying these phenotypes with a combination of adaptive laboratory evolution and high‐throughput proteomics.

Constitutive Activation of RpoH and the Addition of L-arabinose Influence Antibiotic Sensitivity of PHL628 E. coli

“…This advantage is passed onto future generations, increasing a population's resistance to antibiotic treatment. Microbiologists consider antibiotic tolerance an effective stepping stone in developing antibiotic resistance: subpopulations of tolerant bacteria can acquire genetic mutations that confer resistance [3,[10][11][12][13][14][15].…”

Proteome profiling of evolved methicillin-resistant Staphylococcus aureus strains with distinct daptomycin tolerance and resistance phenotypes

“…Proteomics has been proven to be useful in revealing the key players in E. coli persistence and tolerance to various antibiotics ( Hu et al, 2015 ; Sulaiman et al, 2018 ; Sulaiman and Lam, 2020a , b ), and has also been used to investigate persistence and tolerance phenotypes in S. aureus ( Chatterjee et al, 2009 ; Overton et al, 2011 ; Conlon et al, 2013 ; Conlon et al, 2016 ; Zalis et al, 2019 ; Huemer et al, 2021 ; Sulaiman et al, 2021 , 2022 ). Persistence is a phenotype similar to tolerance, but unlike tolerance where most of the cells within the population are tolerant to the drug, persistence describes a situation where the tolerant cells only occur in a small subpopulation, called “persisters” ( Sulaiman and Lam, 2021a , 2022 ).…”

Mutation in the Two-Component System Regulator YycH Leads to Daptomycin Tolerance in Methicillin-Resistant Staphylococcus aureus upon Evolution with a Population Bottleneck

“…Persistence is a phenomenon where tolerance occurs only in a subpopulation of cells called persisters ( 1 , 2 ), which are phenotypic variants with no genetic difference compared to the susceptible cells but are better positioned to withstand antibiotic challenges owing to differential expression of certain genes or proteins and/or shifted metabolism. Although persistence is regarded as a phenotypic trait ( 3 , 4 ), it is known that persistence is highly evolvable. Populations repetitively treated with antibiotics quickly adapt to the treatment and exhibit an increased level of tolerance after merely a few cycles, by accommodating higher fractions of persisters than their progenitors ( 5 ).…”

“…Omics methodology has been recently applied to study the adaptation mechanisms of evolved tolerant and resistant strains from such in vitro evolution experiments ( 4 ), both in E. coli ( 12 , 34 ) and S. aureus ( 13 , 35 – 37 ). Here, we performed quantitative proteomics and compared the proteome profiles of the evolved populations to that of the ancestral strain to gain mechanistic insights into their adaptation.…”