Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing.

ABSTRACT: The applications of whole-metagenome shotgun sequencing (WMGS) in routine clinical analysis are still limited. A combination of a DNA extraction procedure, sequencing, and bioinformatics tools is essential for the removal of human DNA and for improving bacterial species identification in a timely manner. We tackled these issues with a broncho-alveolar lavage (BAL) sample from an immunocompromised patient who had developed severe chronic pneumonia. We extracted DNA from the BAL sample with protocols based either on sequential lysis of human and bacterial cells or on the mechanical disruption of all cells. Metagenomic libraries were sequenced on Illumina HiSeq platforms. Microbial community composition was determined by k-mer analysis or by mapping to taxonomic markers. Results were compared

SUBMITTER: Leo S 

PROVIDER: S-EPMC5618659 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature