. 2021 Feb 20;10(2):209. doi: 10.3390/antibiotics10020209

Table 5.

Advantages and disadvantages of AMR diagnostic methods and technologies.

Method	Advantages	Disadvantages
Conventional methods
Phenotypic methods	Reference, validated methods Simple methodology MIC ¹ values can be estimated Usually, pathogen identification is also achieved	Testing of individual, purified strains Previous cultivation is needed (difficult for fastidious microorganisms, not possible for non-culturable ones) Some disagreements between standards For some taxonomic units, susceptibility cut-off values have not been yet established
Molecular-based assays	Elimination of sample purification Polymicrobial samples analyzed Multiplex targeting of AMR 2 determinants More precise detection and characterization of ARG 3 Relatively quick adaptation to newly introduced resistance factors	Need trained personal Expensive lab equipment Not capable of defining MIC Some ARGs could be missed (sensitivity and coverage) Diversity of ARG poses a difficulty in generating assays due to the cost involved Not total correlation with phenotype
Non-conventional methods
WGS ⁴, WMS ⁵	Adequate for fastidious, non-culturable microorganisms For long-read sequencing platforms, portability and affordability, less laboratory space, and on-site sequencing Genetic basis of AMR established. Novel mechanisms of resistance can be characterized Simultaneous study of multiple AMR determinants (for WMS, from different hosts)	Large equipment costs Complex, laborious methodology Trained personnel needed Sometimes discrepancies with phenotypic tests (false positive, false negative results) For WMS, host of the AMR determinant is not known sometimes Not capable of defining MIC Not total correlation with phenotype
MALDI-TOF MS ⁶	Fast analysis High throughput Automated procedure Simple sample manipulation Low running costs Small sample volume Molecular basis of AMR established	Large equipment costs Testing of individual, purified strains. Previous cultivation is needed Databases (including spectra from resistant and susceptible strains) should be developed Need to find AMR biomarker (peak pattern). Not applicable to all microorganisms Mathematical discrimination procedure needed No portability Not capable of defining MIC
FT-IR ⁷ spectroscopy	Fast analysis High throughput Automated procedure Simple sample manipulation Low running costs Small sample volume	Large equipment costs Testing of individual, purified strains. Previous cultivation is needed Databases (including spectra from resistant and susceptible strains) should be developed Need to find AMR biomarker (spectral pattern). Not applicable to all microorganisms Mathematical discrimination procedure needed No portability IR ⁸ spectra influenced by culture conditions Not capable of defining MIC
Technology
Microfluidics and Lab-on-a-chip (LoC ⁹)	Fast and high throughput analysis Accurate fluid manipulation Low cost, low reagent and power consumption Small sample volume Automated procedure Integration, compactness, portability Easy sample manipulation	Not capable of defining MIC Scalability issues Reproducibility issues in terms of fabrication Large surface to volume ratio Surface treatment (minimize adsorption) Commercialization

¹ MIC: minimal inhibition concentration, ² AMR: antimicrobial resistance, ³ ARG: antimicrobial resistance gene, ⁴ WGS: whole genome sequencing, ⁵ WMS: whole metagenome sequencing, ⁶ MALDI-TOF MS: matrix-assisted laser desorption/ionization- time of flight mass spectrometry, ⁷ FT-IR: Fourier-transform infrared spectroscopy, ⁸ IR: infrared, ⁹ LoC: lab-on-a-chip.