Rapid diagnosis of fatal Nocardia kroppenstedtii bacteremic pneumonia and empyema thoracis by next-generation sequencing: a case report

Nocardia species do not replicate as rapidly other pyogenic bacteria and nocardial infections can be highly fatal, particularly in immunocompromised patients. Here, we present the first report of fatal kroppenstedtii bacteremic pneumonia empyema thoracis diagnosed by next-generation sequencing (NGS) using Oxford Nanopore Technologies' MinION device. The bacterium was identified matrix-assisted laser desorption ionization-time flight mass spectrometry. Due to its low equipment cost, short turn-around-time, portable size, device is a useful platform for NGS routine clinical microbiology laboratories.