ABSTRACTStaphylococcus aureusis subdivided into lineages termed sequence types (STs), infections of which necessitate the expression of virulence factors and metabolic adaptation to the host niche. Given that mechanisms underlying the dynamic replacement of sequence types inS. aureuspopulations have yet to be sufficiently determined, we investigated the role of metabolic determinants in epidemic clones.mleS, encoding the NAD+-dependent malolactic enzyme, was found to be carried by the epidemic clones ST59 and ST398, although not by ST239 and ST5. The genomic location ofmleSin the metabolism-associated region flanked by the thiol-specific redox system and glycolysis operon implies that it plays significant roles in metabolism and pathogenesis. Mouse skin abscess caused by the BS19-mleSmutant strain (isogenicmleSmutant in an ST59 isolate) was significantly attenuated and associated with reductions in interleukin-6 (IL-6) and lactic acid production.mleSdeletion also impairedS. aureusbiofilm formation and survival in RAW264.7 cells. The BS19-mleS-mutant was also characterized by reduced ATP and lactic acid production under microaerobic conditions; however, NAD+/NADH levels remained unaffected.mleSis thus identified as an epidemiological marker that plays an important role in the microaerobic metabolism and pathogenesis of epidemicS. aureusclones.IMPORTANCEGiven the importance of metabolic adaptation during infection, new insights are required regarding the pathogenesis ofS. aureus, particularly for epidemic clones. We accordingly investigated the role of metabolic determinants that are unique to the epidemic clones ST59 and ST398. Our results provide evidence that the NAD+-dependent malolactic enzyme-coding genemleSis an epidemiological marker that plays an important role in the microaerobic metabolism and pathogenesis of epidemicS. aureusclones.