Isolate details. The details of the clinical case have been reported previously (Gao et al., 2010). The first clinical isolate (JKD6210) was susceptible to vancomycin, rifampicin, ciprofloxacin and linezolid; however, after a complicated treatment course including all four of these antibiotics, a small colony variant (SCV JKD6229) was isolated in the spinal aspirate on day 115 after hospital admission. The SCV JKD6229 was a heterogeneous vancomycin-intermediate S. aureus (hVISA) and resistant to rifampicin and ciprofloxacin. It also displayed reduced susceptibility to linezolid. During the 115 days of infection a total of 24 specimens (23 blood cultures and one spinal aspirate) were culture positive for S. aureus. In total, 44 different colony morphologies were isolated from the positive cultures. Details of the isolates selected from these cultures are listed in Table S1 (available in the online Supplementary Material). All isolates were grown on horse blood agar (HBA) or in heart infusion broth at 37 uC unless otherwise stated. Colony size was measured on HBA after 20 h incubation.