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Background:The burden of disease caused by Mycoplasma pneumoniae is unknown in South Africa due to the lack of reliable diagnostic tools and clinicians rarely requesting testing. We sought to describe the prevalence of M. pneumoniae.Methods & Materials: Patients with severe respiratory illness (SRI), influenza-like illness (ILI) and asymptomatic individuals were enrolled from May 2012 to August 2013. Nasopharyngeal/oropharyngeal specimens were collected from all patients; induced sputum was collected from SRI patients only. Real-time PCR targeting the community-acquired respiratory distress syndrome toxin gene (MP181) was used to identify M. pneumoniae. Macrolide susceptibility testing, using high-resolution melt curve analysis (HRM) of the 23S rRNA gene and multiple-locus variablenumber tandem-repeat analysis (MLVA) was performed on 70% (30/43) of M. pneumoniae-positive nasopharyngeal/oropharyngeal specimens. Of these, 80% (24/30) had sufficient volume for culturing. P1 typing was performed on culture-positive specimens using HRM.Results: 3201 SRI patients, 2073 ILI patients and 714 asymptomatic individuals were enrolled, and testing was performed on 71% (2280/3201), 80% (1657/2073) and 74% (525/714) with a detection rate of 2% (46/2280), 1% (15/1657) and 0.2% (1/525), respectively. Among the 46 SRI cases with positive specimens, M. pneumoniae was detected in 24 nasopharyngeal/oropharyngeal specimens, 16 induced sputum specimens and 6 cases were positive in both specimen types. M. pneumoniae was detected in all age groups with 61% (28/46) of cases occurring in children < 5 years. Of those tested using MLVA (73%, 22/30), 3 distinct types, 3/5/6/2 (36%, 8/22), 3/6/6/2 (36%, 8/22) and 4/5/7/2 (27%, 6/22) were identified. Macrolide susceptibility testing results were obtained for 77% (23/30) of M. pneumoniae-positive nasopharyngeal/oropharyngeal specimens, all of which were susceptible. A positive culture for M. pneumoniae was obtained for 13% (3/24) of nasopharyngeal/oropharyngeal specimens, of which two were P1 type 2 and one was P1 type 1.Conclusion: Prevalence of M. pneumoniae was the highest amongst children < 5 years with SRI. No macrolide resistance was detected. Both P1 type 1 and type 2 were present in culture-positive specimens.

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