Metabolic adaptation and microbiota shape Staphylococcus aureus virulence and antimicrobial resistance during intestinal colonization

To study the evolutionary dynamics of MRSA during adaptation in the GI tract of germ-free mice, we introduced MRSA strain USA300 LAC (inoculum size 5 x 108 CFU) into 4 sets of germ-free mice that were housed in independent cages for each set or MRSA strain JH1 by gavage (inoculum size 3 x 108 CFU) into 3 sets of germ-free mice that were housed in independent cages for each set. To identify the genetic basis of adaptation and link genotype to phenotype, for LAC we determined the genomic sequence of the parental strain used as inoculum and ~25 translucent and ~25 opaque colonies from mice in each of the 4 cages five weeks post colonization; for JH1 we sequenced the parental strain and a mixture of translucent and opaque colonies from mice in each of the 3 cages five weeks post colonization.