Overcoming Antibiotic Resistance with Novel Paradigms of Antibiotic Selection

Abstract

Conventional antimicrobial susceptibility tests, including phenotypic and genotypic methods, are insufficiently accurate and frequently fail to identify effective antibiotics. These methods predominantly select therapies based on the antibiotic response of only the lead bacterial pathogen within pure bacterial culture. However, this neglects the fact that, in the majority of human infections, the lead bacterial pathogens are present as a part of multispecies communities that modulate the response of these lead pathogens to antibiotics and that multiple pathogens can contribute to the infection simultaneously. This discrepancy is a major cause of the failure of antimicrobial susceptibility tests to detect antibiotics that are effective in vivo. This review article provides a comprehensive overview of the factors that are missed by conventional antimicrobial susceptibility tests and it explains how accounting for these methods can aid the development of novel diagnostic approaches.

Keywords: TezR; antibiotic resistance; antimicrobial susceptibility tests; bacterial pathogens; biofilm; collective antibiotic resistance; persisters.

Figure 1

Reprinted with permission from ref. [144]. AtbFinder principle of operation and performance. An illustrated schematic of the AtbFinder performance protocol developed for different biosamples. (1) A biosample, which can be optionally diluted with sterile water, is plated onto the wells of multi-well AtbFinder plates (here, for the representation purposes we depicted a 12-well plate). The testing wells contain TGV nutrient agar supplemented with antibiotics (one or several antibiotics per well) selected as per current therapeutic guidelines and added to the medium at concentrations clinically achievable at the site of infection. Two control wells contain antibiotic-free TGV agar. (2) Plate reading is performed following sampling and incubation at 37 °C for 4 h. The presence of microbial growth is identified with the naked eye and can be confirmed with a stereoscopic microscope. Microbial growth in any testing well means that the antibiotic that has been added to the nutrient medium in this well is “ineffective”. The absence of bacterial growth in the well enables categorization of the antibiotic(s) present in the well as “effective”.