Figure 1. Figure 1. Clinical Course of the 14-Year-Old Patient with Fulminant Meningoencephalitis. Panel A shows a timeline beginning with the patient's trip to Puerto Rico in August 2012 and ending after his recovery in October 2013. Major events during the course of the patient's illness are indicated by arrows. Panel B shows laboratory values obtained and pertinent medications administered during the patient's third hospitalization. The upper graph shows the body-temperature curve (red line) and peripheral-blood leukocyte counts (purple bars). The lower graph shows the leukocyte count and differential (bars) and the glucose (dashed line) and protein (solid line) levels in serially collected cerebrospinal fluid samples. The horizontal thick gray lines show the medications administered. The asterisk denotes the first course of cefuroxime (CFX) given to the patient, which did not result in clinical improvement. CFPM denotes cefepime, EVD extraventricular drain, MEP methylprednisolone, MRI magnetic resonance imaging, PCN G penicillin G, PEG-ADA polyethylene glycol–modified adenosine deaminase, and VANC vancomycin.

A 14-year-old boy with severe combined immunodeficiency (SCID) caused by adenosine deaminase deficiency and partial immune reconstitution after he had undergone two haploidentical bone marrow transplantations initially presented to the emergency department in early April 2013 after having had headache and fevers, with temperatures up to 39.4°C, for 6 days (Figure 1A). He was admitted to the hospital and discharged 1 day later after resolution of his fever and headache.

The patient's outpatient medications included monthly infusions of intravenous immune globulin for hypogammaglobulinemia and trimethoprim–sulfamethoxazole or atovaquone for prophylaxis against Pneumocystis jirovecii pneumonia. He had no known sick contacts but did have three pet cats. He had gone on a missionary trip to Puerto Rico during the first 2 weeks of August 2012 (Figure 1A), where he swam in a river and the ocean. Notably, a 17-year-old fellow traveler had been hospitalized for 4 days with fever and hematuria. The patient had also vacationed in Florida in March 2013, where he swam in a pool at a resort where there were a number of feral cats.

In September 2012, the patient had presented to his primary care physician with fever, headache, and bilateral conjunctivitis that resolved spontaneously in 10 days (Figure 1A). At the end of October 2012, he had had photophobia and pain with movement of his left eye. His ophthalmologist had prescribed eyedrops consisting of a combination of a glucocorticoid, a vasoconstrictor, and an antibiotic (ciprofloxacin) for uveitis. One week later, uveitis had developed in the contralateral eye and was treated in a similar manner. The ophthalmologic symptoms had resolved by December 2012. Thrombocytopenia had also developed in October 2012, and the patient was treated with rituximab for presumed immune thrombocytopenic purpura, with subsequent normalization of his platelet counts.

After the brief hospitalization in early April 2013, the patient was readmitted to the hospital at the end of April 2013 with fever, photophobia, and daily frontotemporal headaches (Figure 1A). In addition, he reported increasing fatigue, abdominal pain, and a weight loss of 2.3 kg. On admission, he had normal vital signs, and the physical examination was unremarkable. The peripheral-blood leukocyte count was 3800 per cubic millimeter with 78% neutrophils. The erythrocyte sedimentation rate was 39 mm per hour (normal range, 0 to 20 mm per hour). The deoxyadenosine nucleotide percentage in the red cells, a measure of control of adenosine deaminase deficiency, was 5.9% (target range, <10%). Serum electrolyte, creatinine, liver-enzyme, and IgG values were within normal ranges. Analysis of the cerebrospinal fluid (CSF) showed 125 leukocytes per cubic millimeter (18% neutrophils and 52% lymphocytes), 0 red cells, a protein level of 97 mg per deciliter (normal range, 15 to 45 mg per deciliter), and a glucose level of 24 mg per deciliter (1.3 mmol per liter; normal range, 40 to 85 mg per deciliter [2.2 to 4.7 mmol per liter]) (Figure 1B). The results of magnetic resonance imaging (MRI) of the head were unremarkable.

An extensive infectious disease workup was unrevealing (Table S1 in the Supplementary Appendix, available with the full text of this article at NEJM.org). Given the low suspicion for bacterial meningitis, the patient received no empirical antimicrobial agents. He was discharged with instructions to continue his routine prophylaxis and monthly intravenous immune globulin therapy. In May and June, his symptoms waxed and waned but were mild enough to allow him to return to school.

The patient was admitted in July for a third time with fever, headache, diffuse weakness, myalgias, nausea, and vomiting (Figure 1A and 1B). He received two doses of rituximab for possible autoimmune involvement but had no reduction of symptoms. MRI of the head on admission showed patchy, nonenhancing, T 2 -weighted hyperintensities in the basal ganglia bilaterally. Analysis of CSF showed 109 leukocytes per cubic millimeter (16% neutrophils and 38% lymphocytes), 0 red cells, a protein level of 162 mg per deciliter, and a glucose level of 17 mg per deciliter (0.9 mmol per liter). The level of angiotensin-converting enzyme (ACE) in CSF was elevated at 7.2 U per liter (normal value, <2.5 U per milliliter).

Figure 2. Figure 2. Neuroradiologic MRI and Brain-Biopsy Findings. The images shown in Panels A, B, and C were acquired on day 13 of the patient's third hospitalization, whereas the image shown in Panel D was acquired on day 55, after the patient had completed a 7-day course of intravenous penicillin G. An axial T 2 -weighted image of the head revealed persistent hyperintensities in the basal ganglia and deep frontal white matter (Panel A, arrows). Sagittal and axial T 2 -weighted fluid-attenuated inversion recovery (FLAIR) images (Panels B and C, respectively) showed thickening in and around the basilar meninges (arrows). An axial T 2 -weighted FLAIR image (Panel D) depicts near resolution of the previously seen (Panels B and C) basilar meningitis. Results of a biopsy of the right frontal lobe performed 2 weeks after the third hospital admission showed infiltration by lymphocytes and epithelioid histiocytes in the subarachnoid space with a perivascular predilection (Panel E, hematoxylin and eosin). T lymphocytes were visualized by means of immunolabeling with anti-CD3 antibody (Panel F). Various stains also showed the absence of mycobacteria (Panel G, acid-fast), fungi (Panel H, Gomori methenamine silver), and leptospira or other spirochetes (Panel I, Warthin–Starry silver). Electron microscopy revealed the presence of an inflammatory infiltrate and the absence of inclusion bodies, viral particles, or other evidence of microorganisms (Panel J).

A repeat MRI of the head at day 13 showed persistent hyperintensities in the basal ganglia and interval development of basilar leptomeningitis extending into the cerebral hemispheres (Figure 2A, 2B, and 2C). Given these MRI findings and the lack of clinical improvement, a biopsy of the right frontal lobe was performed 2 weeks after admission. Histologic examination revealed inflamed leptomeninges with a granulomatous infiltrate (Figure 2E). The cerebral cortex was normal with the exception of two microscopic foci of microglial proliferation. Immunohistochemical testing confirmed the presence of CD3-positive T cells (Figure 2F) and CD68-positive histiocytes and the absence of CD20-positive B lymphocytes. Immunohistochemical testing and electron microscopy did not identify fungi, bacteria, or viruses (Figure 2G through 2J).

Given the negative results of the infectious disease workup (Table S1 in the Supplementary Appendix), the elevated ACE level in CSF, the patient's history of presumed autoimmune disease, and the presence of granulomatous leptomeningitis, the patient was treated with intravenous glucocorticoids for possible neurosarcoidosis. Treatment with polyethylene glycol–modified adenosine deaminase (PEG-ADA) was also administered in an attempt to boost his immune system.10 Despite these interventions, the patient's condition continued to decline, with new-onset psychiatric symptoms. An extraventricular drain was placed because of worsening hydrocephalus, and the patient was placed in a medically induced coma to control new-onset status epilepticus. Cefuroxime, administered as prophylaxis against infection at the site of the extraventricular drain, had no effect on his CSF values or clinical status (Figure 1B).

Figure 3. Figure 3. Diagnosis of Leptospira Infection by Means of Unbiased Next-Generation Sequencing (NGS). A clinical laboratory workflow for a comprehensive pathogen-detection assay with the use of unbiased NGS is shown (Panel A). The total time required for the bioinformatics analysis of NGS data, 97 minutes (pie chart, inset), was only 3.4% of the 48-hour turnaround time for the assay. Sequence-based ultra-rapid pathogen identification (SURPI) is a bioinformatics pipeline for pathogen identification from data obtained by means of next-generation sequencing of clinical samples. In de novo assembly, overlapping sequence reads are joined together in order to create longer contiguous sequences. The overhead time refers to computational time necessary for file-format conversion, sequence retrieval of identified matches in the database, and taxonomic classification of aligned reads. A total of 475 sequence reads derived from the patient's cerebrospinal fluid (CSF) sample were mapped to the closest matched leptospira genome in the reference database, Leptospira borgpetersenii (Panel B). The distribution of bacterial and viral sequences identified in the patient's CSF included propionibacteria, anelloviruses, and bacteriophages, which are generally considered to be nonpathogenic body flora (Panel C). Phylogenetic analysis of the full-length gene rpoB showed sequences from representative serovars, strains, and species of leptospira, highlighting the strain identified in the patient with fulminant meningoencephalitis (provisionally named L. santarosai strain UW [University of Wisconsin]) (Panel D). The scale bar denotes the number of nucleotide substitutions per site. GenBank accession numbers are provided in the Supplementary Appendix.

Table 1. Table 1. Confirmatory Diagnostic Testing for Neuroleptospirosis.

After written informed consent was obtained from a parent on behalf of the patient, he was enrolled in a research study for pathogen detection and discovery in hospitalized patients with the use of unbiased next-generation sequencing. Coincident with sending CSF and serum samples for next-generation sequencing, broad-spectrum antimicrobial coverage with cefepime and vancomycin was started empirically for fever suggestive of a potential nosocomial infection (Figure 1B). Within 48 hours after receipt of the samples (Figure 3A), next-generation sequencing analysis of more than 8 million sequences with the use of a bioinformatics pipeline for the detection of all known pathogens detected sequence reads corresponding to leptospira infection in the patient's CSF but not in the serum. Although the identification of leptospira in the CSF was later confirmed with the use of targeted PCR and Sanger sequencing by two independent laboratories (Table 1), a decision was made to treat the patient immediately for neuroleptospirosis before confirmatory testing could be obtained. Therefore, glucocorticoids were tapered, and antibiotic coverage was narrowed to high-dose intravenous penicillin G (13 million units daily).

The patient gradually recovered over the next 7 days, with resolution of his status epilepticus, normalization of his CSF, and resolution of leptomeningitis as observed on serial MRI scans (Figure 1A, 1B, and 2D). He was discharged to inpatient rehabilitation 14 days after completing a 7-day course of intravenous penicillin G. At discharge, the patient had largely recovered but still had occasional right facial twitching from simple partial seizures. After 11 days of rehabilitation, he returned home near the end of September (76 days after hospital admission) close to his premorbid functional status. CSF collected 4 months later revealed 0 leukocytes and red cells, a protein level of 49 mg per deciliter, and a glucose level of 47 mg per deciliter (2.6 mmol per liter); the CSF was negative for leptospira on repeat PCR testing (Table 1).