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Background  Methicillin resistant  Staphylococcus aureus  (MRSA) strains were once confined to hospitals however, in the last 20 years MRSA infections have emerged in the community in people with no prior exposure to hospitals. Strains causing such infections were novel and referred to as community-associated MRSA (CA-MRSA). The aim of this study was to determine the MRSA carriage rate in children in eastern Uganda, and to investigate coexistence between CA-MRSA and hospital-associated (HA-MRSA).    Methods  Between February and October 2011, nasopharyngeal samples (one per child) from 742 healthy children under 5 years in rural eastern Uganda were processed for isolation of MRSA, which was identified based on inhibition zone diameter of ≤19 mm on 30 μg cefoxitin disk. SCC mec  and  spa  typing were performed for MRSA isolates.    Results  A total of 140  S. aureus  isolates (18.9%, 140/742) were recovered from the children of which 5.7% (42/742) were MRSA. Almost all (95.2%, 40/42) MRSA isolates were multidrug resistant (MDR). The most prevalent SCC mec  elements were types IV (40.5%, 17/42) and I (38.1%, 16/42). The overall frequency of SCC mec  types IV and V combined, hence CA-MRSA, was 50% (21/42). Likewise, the overall frequency of SCC mec  types I, II and III combined, hence HA-MRSA, was 50% (21/42). Spa types t002, t037, t064, t4353 and t12939 were detected and the most frequent were t064 (19%, 8/42) and t037 (12%, 5/42).    Conclusion  The MRSA carriage rate in children in eastern Uganda is high (5.7%) and comparable to estimates for Mulago Hospital in Kampala city. Importantly, HA-MRSA (mainly of  spa  type t037) and CA-MRSA (mainly of  spa  type t064) coexist in children in the community in eastern Uganda, and due to high proportion of MDR detected, outpatient treatment of MRSA infection in eastern Uganda might be difficult.    Electronic supplementary material  The online version of this article (10.1186/s13756-019-0551-1) contains supplementary material, which is available to authorized users.

CA-MRSA and HA-MRSA coexist in community and hospital settings in Uganda