Epidemiology and Molecular Identification and Characterization of Mycoplasma pneumoniae, South Africa, 2012–2015

During 2012–2015, we tested respiratory specimens from patients with severe respiratory illness (SRI), patients with influenza-like illness (ILI), and controls in South Africa by real-time PCR for Mycoplasma pneumoniae, followed by culture and molecular characterization of positive samples. M. pneumoniae prevalence was 1.6% among SRI patients, 0.7% among ILI patients, and 0.2% among controls (p<0.001). Age <5 years (adjusted odd ratio 7.1; 95% CI 1.7–28.7) and HIV infection (adjusted odds ratio 23.8; 95% CI 4.1–138.2) among M. pneumonia–positive persons were associated with severe disease. The detection rate attributable to illness was 93.9% (95% CI 74.4%–98.5%) in SRI patients and 80.7% (95% CI 16.7%–95.6%) in ILI patients. The hospitalization rate was 28 cases/100,000 population. We observed the macrolide-susceptible M. pneumoniae genotype in all cases and found P1 types 1, 2, and a type 2 variant with multilocus variable number tandem repeat types 3/6/6/2, 3/5/6/2, and 4/5/7/2.