organism: clinical metagenome
description: A 14-year-old boy from Wisconsin with severe combined immunodeficiency presented 3 times to a medical facility over 4 months with fever and headache that progressed to hydrocephalus and status epilepticus necessitating a medically-induced coma.  An exhaustive diagnostic workup including brain biopsy was unrevealing.  Within 48 hours after receipt of the sample, unbiased next-generation sequencing of the patient's cerebrospinal fluid and computational analysis using an ultra-rapid pipeline for comprehensive pathogen detection identified 475 of 8,187,737 sequences corresponding to Leptospira, confirmed as Leptospira santarosai by PCR testing performed in an independent laboratory and phylogenetic analysis.  All previously validated clinical assays for leptospirosis were negative.  The patient responded dramatically when treated with appropriate antimicrobials, and he was discharged home 24 days later near his premorbid baseline.
attributes.tag: strain
attributes.value: UW
attributes.tag: geo_loc_name
attributes.value: USA: University of Wisconsin
attributes.tag: host
attributes.value: Homo sapiens
attributes.tag: isolation_source
attributes.value: cerebrospinal fluid and serum
attributes.tag: investigation_type
attributes.value: miens-culture
attributes.tag: label
attributes.value: Clinical sample from infected human
attributes.tag: collection_date
attributes.value: missing
attributes.tag: disease
attributes.value: encephalitis