16S rRNA sequencing for antimicrobial susceptibility testing

The current technologies to profile antimicrobial susceptibility are time-consuming. The disc diffusion method, the microdilution method or the time-kill method visually check the growth of single bacterial strain cultured in the presence of antibiotics in agar medium or liquid medium. Recent advances in sequencing technology have made it possible to determine bacterial abundance easily even in complex community. In this study, we reasoned measuring bacterial abundance by sequencing instead of colony counting can be applied to antibiotic susceptibility test. The absolute abundances of test strains in culture before and after exposure to antibiotics were measured by using Nanopore sequencing of 16S rRNA amplicons. This sequencing data allowed us to classify the test strains into three groups based on antibiotic susceptibility: normally proliferating bacteria (no antibacterial activity), non-proliferating bacteria (bacteriostatic activity), and dead or dying bacteria (final count less than initial cell count; bactericidal activity).