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Background   Staphylococcus aureus  ( S.aureus ) is a major cause of both healthcare and community acquired infections. In developing countries, manual phenotypic tests are the mainstay for the identification of staphylococci with the tube and slide coagulase tests being relied upon as confirmatory tests for  S. aureus . The subjectivity associated with interpretation of these tests may result in misidentification of coagulase negative staphylococci as  S.aureus . Given that antibiotic resistance is more prevalent in CONS, this may result in over estimation of methicillin resistant  S.aureus  (MRSA) prevalence.    Methods  A review of susceptibility data from all non-duplicate  S.aureus  isolates generated between March 2011 and May 2013 by the Vitek-2 (bioMérieux) automated system was performed by the authors. The data was generated routinely from processed clinical specimens submitted to the microbiology laboratories for culture and sensitivity at the Aga Khan University Hospital and Gertrude’s children’s hospital both situated in Nairobi.    Results  Antimicrobial susceptibility data from a total of 731 non-duplicate  S.aureus  isolates was reviewed. Majority (79.2%) of the isolates were from pus swabs. Only 24 isolates were both cefoxitin and oxacillin resistant while 3 were resistant to oxacillin but susceptible to cefoxitin giving an overall MRSA prevalence of 3.7% (27/731). None of the isolates were resistant to mupirocin, linezolid, tigecycline, teicoplanin or vancomycin.    Conclusion  The prevalence of MRSA in this study is much lower than what has been reported in most African countries. The significant change in antibiotic susceptibility compared to what has previously been reported in our hospital is most likely a consequence of the transition to an automated platform rather than a trend towards lower resistance rates.    Electronic supplementary material  The online version of this article (doi:10.1186/s12879-014-0669-y) contains supplementary material, which is available to authorized users.

bmc infectious diseases

Low prevalence of methicillin resistant Staphylococcus aureus as determined by an automated identification system in two private hospitals in Nairobi, Kenya: a cross sectional study