Pathogen identification is indeed a very exciting application for NGS. In case you're interested, here[0] is a paper about a tool called SURPI (Sequence-based Ultra-Rapid Pathogen Identification) which was designed for that purpose. Also, here[1] is a case report from the NEJM where SURPI was used to diagnose a patient with Neuroleptospirosis, which allowed him to be treated quickly and eventually recover. SURPI isn't the only horse in this game, of course, but I've worked with it before so it immediately came to mind.
[0]: "A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples" http://genome.cshlp.org/content/24/7/1180.long
[0]: "A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples" http://genome.cshlp.org/content/24/7/1180.long
[1]: "Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing" http://www.nejm.org/doi/full/10.1056/NEJMoa1401268