Antibiotic-resistant bacteria like carbapenem-resistant Enterobacteriaceae (CRE) pose a serious threat to human health. Some resistant pathogens can exist alongside our commensal microbiota at undetectable levels. Antibiotic use can lead to outgrowth of these subclinically colonized bacteria. A recent study sought to better understand the interaction between the gut microbiota and CRE during subclinical colonization and outgrowth. First, researchers exposed wild-type mice to the CRE K. pneumoniae. While the levels of K. pneumoniae were not detectable after exposure, the post-exposure microbiome was disrupted. Then, administration of an antibiotic cocktail, ampicillin, vancomycin, or azithromycin induced K. pneumoniae outgrowth while reducing overall microbial diversity. Vancomycin only induced outgrowth in a subset of mice. The researchers found these outgrowth-susceptible mice had differences in mRNA stability pathways and xylose abundance. While more work is needed to determine if findings in this model can extend to humans, this new model can be used to test the subclinical colonization and outgrowth of other pathogens, and this study identified potential markers for K. pneumoniae outgrowth susceptibility.