The diagnosis of bacterial infections continues to rely on culture, a slow process in which antibiotic susceptibility profiles of potential pathogens are made available to clinicians 48 hours after sampling, at best. Recently, clinical metagenomics, the metagenomic sequencing of samples with the purpose of identifying microorganisms and determining their susceptibility to antimicrobials, has emerged as a potential diagnostic tool that could prove faster than culture. Clinical metagenomics indeed has the potential to detect antibiotic resistance genes (ARGs) and mutations associated with resistance. Nevertheless, many challenges have yet to be overcome in order to make rapid phenotypic inference of antibiotic susceptibility from metagenomic data a reality.

The objective of this narrative review is to discuss the challenges underlying the phenotypic inference of antibiotic susceptibility from metagenomic data.

We conducted a narrative review using published articles available in the National Center for Biotechnology Information PubMed database.

We review the current ARG databases with a specific emphasis on those which now provide associations with phenotypic data. Next, we discuss the bioinformatic tools designed to identify ARGs in metagenomes. We then report on the performance of phenotypic inference from genomic data and the issue predicting the expression of ARGs. Finally, we address the challenge of linking an ARG to this host.

Significant improvements have recently been made in associating ARG and phenotype, and the inference of susceptibility from genomic data has been demonstrated in pathogenic bacteria such as Staphylococci and Enterobacterales. Resistance involving gene expression is more challenging however, and inferring susceptibility from species such as Pseudomonas aeruginosa remains difficult. Future research directions include the consideration of gene expression via RNA sequencing and machine learning.