The need for new antimicrobials to treat bacterial infections has led to the use of type II fatty acid synthesis (FASII) enzymes as front-line targets. However, recent studies suggest that FASII inhibitors may not work against the opportunist pathogen Staphylococcus aureus, as environmental fatty acids favor emergence of multi-anti-FASII resistance. As fatty acids are abundant in the host and one FASII inhibitor, triclosan, is widespread, we investigated whether fatty acid pools impact resistance in clinical and veterinary S. aureus isolates. Simple addition of fatty acids to the screening medium led to a 50% increase in triclosan resistance, as tested in 700 isolates. Moreover, nonculturable triclosan-resistant fatty acid auxotrophs, which escape detection under routine conditions, were uncovered in primary patient samples. FASII bypass in selected isolates correlated with polymorphisms in the acc and fabD loci. We conclude that fatty-acid-dependent strategies to escape FASII inhibition are common among S. aureus isolates and correlate with anti-FASII resistance and emergence of nonculturable variants.KEYWORDS antibiotic resistance, infection, persistence, nondetectable resistance, fatty acids, Staphylococcus aureus S taphylococcus aureus is a leading cause of a wide range of infections that can affect numerous host organs and cause a range of effects from mild symptoms to severe and life-threatening diseases. Acquisition of antimicrobial resistance, likely due to overuse of antibiotics, is the principal cause of S. aureus drug resistance (1). A class of new-generation antimicrobials in intensive development uses the type II fatty acid synthesis (FASII) pathway as an antibacterial target (2-5) to treat S. aureus infections (6-8). A widely used biocide, triclosan (5-chloro-2-[2,4-dichlorophenoxy]phenol; commercialized as Irgasan or Microban), is a prototype for further anti-FASII development (4, 9, 10).The utility of FASII inhibitors was questioned when several Gram-positive bacteria were shown to be refractory to FASII inhibitors in the presence of exogenous fatty acids, making FASII enzymes dispensable (11,12). Both free and complexed fatty acids are abundant in the host (13,14), which would facilitate FASII bypass. Reservoirs and invasion sites of clinical and community-acquired staphylococci (i.e., skin, nares, gut, blood, and organs) are naturally rich in fatty acids (13-16), and triclosan is present in the environment and in human body fluids (17,18). This combination could favor FASII bypass via emergence of triclosan-resistant variants, including fatty acid auxotrophs. Fatty-acid-dependent isolates escape detection on standard isolation media, thereby confounding diagnosis and treatment.