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Background Previous studies have different viewpoints about the clinical impact of methicillin resistance on mortality of hospital-acquired bloodstream infection (BSI) patients with Staphylococcus aureus (S.aureus).The objective of this study was to investigate the mortality of hospital-acquired BSI with S.aureus in a military hospital and analyze the risk factors for the hospital mortality.Methods A retrospective cohort study was performed in patients admitted to the biggest military tertiary teaching hospital in China between January 2006 and May 2011.All included patients had clinically significant nosocomial BSI with S.aureus.Multivariate Logistic regression analysis was used to identify the risk factors for hospital mortality of patients with S.aureus BSI.Results One hundred and eighteen patients of more than one year old were identified as clinically and microbiologically confirmed nosocomial bacteraemia due to S.aureus,and 75 out of 118 patients were infected with methicillin-resistant S.aureus (MRSA).The overall mortality of nosocomial S.aureus BSI was 28.0％.Methicillin resistance in S.aureus bacteremia was associated with significant increase in the length of hospitalization and high proportion of inappropriate empirical antibiotic treatment.After Logistic regression analysis,the severity of clinical manifestations (APACHE Ⅱ score) (odds ratio (OR) 1.22,95％ confidence interval (CI) 1.12-1.34) and inadequacy of empirical antimicrobial therapy (OR 0.25,95％ CI 0.09-0.69) remained as risk factors for hospital mortality.Conclusions Nosocomial S.aureus BSI was associated with high in-hospital mortality.Methicillin resistance in S.aureus has no significant impact on the outcome of patients with staphylococcal bacteremia.Proper empirical antimicrobial therapy is very important to the prognosis.