Genetic Epidemiology and Resistance Investigations of Clinical Yeasts in Alexandria, Egypt

Yeast bloodstream infections lead to high mortality and morbidity and are mostly observed in immunocompromised patients. In Africa, only a few studies have characterized clinical yeasts. To increase insight into yeast resistance and transmission in Africa, we identified various yeasts from Alexandria, Egypt and performed antifungal susceptibility testing (AFST) and genotyping. A total of 1307 single isolates from unique patients, recovered from different anatomical sites including the bloodstream, retrieved from a reference laboratory in Alexandria, Egypt were studied. All isolates were identified with MALDI-TOF MS, while some were initially identified with a Vitek 2 Compact system. Short tandem repeat (STR) genotyping was performed for the most common species, and AFST was performed with microbroth dilution. Among bloodstream isolates (n = 71), C. albicans was the most common etiological agent, followed by C. tropicalis and C. parapsilosis. Comparison of yeast identification methods demonstrated that 22% of isolates were incorrectly identified with the Vitek 2 Compact system compared to MALDI-TOF MS. Multiple rare yeasts showed reduced antifungal susceptibility. STR genotyping demonstrated potential events of nosocomial transmission with N. glabratus and C. parapsilosis. Moreover, an azole-resistant C. tropicalis clade identified earlier in Alexandria was still present. To conclude, clinical yeasts in Alexandria, Egypt, are overall susceptible common species.