Detection of bacterial pathogens from broncho-alveolar lavage by next-generation sequencing. Leo S

The application of culture-free methods, notably whole-metagenome shotgun (WMGS) sequencing, in routine clinical analysis is still limited although they have some advantage over culture-based approach. A combination of an appropriate DNA extraction procedure, sequencing and bioinformatics tools is essential for removal of human DNA and improved bacterial species identification. We tackled these issues by applying a specifically-designed clinical metagenomics pipeline, from DNA extraction to bioinformatics methods, on a broncho-alveolar lavage (BAL) sample from a severely immunocompromised patient who developed an atypical nosocomial pneumonia.