Antimicrobial resistance hidden within multi-serovar Salmonella populations.

Salmonella can exist in food animals as multi-serovar populations, and different serovars can harbor diverse antimicrobial resistance (AMR) profiles. Conventional Salmonella isolation only assesses AMR in the most abundant members of a multi-serovar population, which typically reflects their relative abundance in the initial sample. Therefore, AMR in underlying serovars is an undetected reservoir that can readily be expanded upon antimicrobial use. CRISPR-SeroSeq profiling demonstrated that 60% of cattle fecal samples harbored multiple serovars, including low levels of serovar Reading in 11% samples, which were not found by culture-based Salmonella isolation. An in-vitro challenge revealed serovar Reading was tetracycline-resistant, while more abundant serovars were susceptible. This study highlights the importance of AMR surveillance in multi-serovar populations.