A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification.

Metagenomic next-generation sequencing (mNGS) holds promise as a diagnostic tool for unbiased pathogen identification and precision medicine. However, its medical utility depends largely on assay simplicity and reproducibility. In the current study, we aimed to develop a streamlined Illumina and Oxford Nanopore-based DNA/RNA library preparation protocol and rapid data analysis pipeline. The Illumina sequencing-based mNGS method was first developed and evaluated using a set of samples with known aetiology. Its sensitivity for RNA viruses (influenza A, H1N1) was < 6.4 × 102 EID50/mL, and a good correlation between viral loads and mapped reads was observed. Then, the rapid turnaround time of Nanopore sequencing was tested by sequencing influenza A virus and adenoviruses. Furthermore, 11 respiratory swabs or sputum samples pre-tested for a panel of pathogens were analysed, and the pathogens identified by Illumina sequencing showed 81.8% concordance with qPCR results. Additional sequencing of cerebrospinal fluid (CSF) samples from HIV-1-positive patients with meningitis/encephalitis detected HIV-1 RNA and Toxoplasma gondii sequences. In conclusion, we have developed a simplified protocol that realizes efficient metagenomic sequencing of a variety of clinical samples and pathogen identification in a clinically meaningful time frame.

The metagenomic next-generation sequencing in diagnosing central nervous system angiostrongyliasis: a case report.

BACKGROUNDS: The incidence of angiostrongyliasis is increasing in recent decades due to the expanding endemic areas all over the world. Clinicians face tremendous challenge of diagnosing angiostrongyliasis because of the lack of awareness of the disease and less effective definitive laboratory tests. CASE PRESENTATION: A 27-year-old man initially manifested skin itching, emesis, myalgia and quadriparesis. With progressive weakness of four limbs and elevated protein in the cerebrospinal fluid (CSF), he was diagnosed as Guillain-Barré syndrome and treated with intravenous methylprednisolone and immunoglobulin. However, the patient deteriorated with hyperpyrexia, headache and then persistent coma. The routine tests for Angiostrongylus cantonensis (A. cantonensis) with both the CSF and the serum were all negative. In contrast, the metagenomic next-generation sequencing (mNGS) was applied with the serum sample and the CSF sample in the middle phase. The central nervous system (CNS) angiostrongyliasis was diagnosed by mNGS with the mid-phase CSF, but not the mid-phase serum. At the same time, the CSF analysis revealed eosinophils ratio up to 67%. The discovery of A. cantonensis was confirmed by PCR with CSF later. Unfortunately, the patient died of severe angiostrongyliasis. During his hospitalization, mNGS was carried out repeatedly after definitive diagnosis and targeted treatment. The DNA strictly map reads number of A. cantonensis detected by mNGS was positively correlated with the CSF opening pressure and clinical manifestations. CONCLUSIONS: The case of A. cantonensis infection highlights the benefit of mNGS as a target-free identification in disclosing the rare CNS angiostrongyliasis in the unusual season, while solid evidence from routine clinical testing was absent. The appropriate sample of mNGS should be chosen according to the life cycle of A. cantonensis. Besides, given the fact that the DNA reads number of A. cantonensis fluctuated with CSF opening pressure and clinical manifestations, whether mNGS could be applied as a marker of effectiveness of treatment is worth further exploration.

The complex health seeking pathway of a human African trypanosomiasis patient in Côte d'Ivoire underlines the need of setting up passive surveillance systems.

BACKGROUND: Significant efforts to control human African trypanosomiasis (HAT) over the two past decades have resulted in drastic decrease of its prevalence in Côte d'Ivoire. In this context, passive surveillance, integrated in the national health system and based on clinical suspicion, was reinforced. We describe here the health-seeking pathway of a girl who was the first HAT patient diagnosed through this strategy in August 2017. METHODS: After definitive diagnosis of this patient, epidemiological investigations were carried out into the clinical evolution and the health and therapeutic itinerary of the patient before diagnosis. RESULTS: At the time of diagnosis, the patient was positive in both serological and molecular tests and trypanosomes were detected in blood and cerebrospinal fluid. She suffered from important neurological disorders. The first disease symptoms had appeared three years earlier, and the patient had visited several public and private peripheral health care centres and hospitals in different cities. The failure to diagnose HAT for such a long time caused significant health deterioration and was an important financial burden for the family. CONCLUSION: This description illustrates the complexity of detecting the last HAT cases due to complex diagnosis and the progressive disinterest and unawareness by both health professionals and the population. It confirms the need of implementing passive surveillance in combination with continued sensitization and health staff training.

Next-generation sequencing of cerebrospinal fluid for the diagnosis of neurocysticercosis.

OBJECTIVE: Neurocysticercosis (NCC) is the most common parasitic disease of the human central nervous system (CNS). However, a diagnosis of NCC may be hard to make if the specific clinical and routine neuroimaging manifestations are lacking, which hinders physicians from considering further immunodiagnostic tests. PATIENTS AND METHODS: Seven patients presented with fever, headache, nausea, cognitive decline, confusion, or progressive leg weakness. There were no pathogens found in the cerebrospinal fluid (CSF); patients were clinically suspected of meningoencephalitis or cerebrovascular disease. To clearly determine the etiology, next generation sequencing (NGS) of the CSF was used to detect pathogens in these seven patients. RESULTS: Taenia solium DNA sequences were detected in the seven patients, but not in the non-template controls (NTCs) or the other patients with clinically suspected CNS infections. Based on the patients' medical data and the diagnostic criteria for NCC, seven patients were diagnosed with probable NCC. The unique reads aligning to Taenia solium ranged from 6 to 261064, with genomic coverage ranging from 0.0003% to 14.8079%. The number of unique reads and genomic coverage dropped in three of the seven patients after antiparasitic treatment, consistent with the relief of symptoms. CONCLUSION: This study showed that NGS of the CSF might be an auxiliary diagnostic method for NCC patients. Larger studies are required.

Balamuthia mandrillaris-Related Primary Amoebic Encephalitis in China Diagnosed by Next Generation Sequencing and a Review of the Literature.

BACKGROUND: Encephalitis is caused by infection, immune mediated diseases, or primary inflammatory diseases. Of all the causative infectious pathogens, 90% are viruses or bacteria. Granulomatous amoebic encephalitis (GAE), caused by Balamuthia mandrillaris, is a rare but life-threatening disease. Diagnosis and therapy are frequently delayed due to the lack of specific clinical manifestations. METHOD: A healthy 2 year old Chinese male patient initially presented with a nearly 2 month history of irregular fever. We present this case of granulomatous amoebic encephalitis caused by B. mandrillaris. Next generation sequencing of the patient's cerebrospinal fluid (CSF) was performed to identify an infectious agent. RESULT: The results of next generation sequencing of the CSF showed that most of the mapped reads belonged to Balamuthia mandrillaris. CONCLUSION: Next generation sequencing (NGS) is an unbiased and rapid diagnostic tool. The NGS method can be used for the rapid identification of causative pathogens. The NGS method should be widely applied in clinical practice and help clinicians provide direction for the diagnosis of diseases, especially for rare and difficult cases.

Association of TRAF1/C5 Locus Polymorphisms with Epilepsy and Clinical Traits in Mexican Patients with Neurocysticercosis.

Neurocysticercosis is caused by the establishment of Taenia solium cysts in the central nervous system. Murine cysticercosis by Taenia crassiceps is a useful model of cysticercosis in which the complement component 5 (C5) has been linked to infection resistance/permissiveness. This work aimed to study the possible relevance for human neurocysticercosis of single nucleotide polymorphisms (SNPs) in the C5-TRAF1 region (rs17611 C/T, rs992670 G/A, rs25681 G/A, rs10818488 A/G, and rs3761847 G/A) in a Mexican population and associated with clinical and radiological traits related to neurocysticercosis severity (cell count in the cerebrospinal fluid [CSF cellularity], parasite location and parasite load in the brain, parasite degenerating stage, and epilepsy). The AG genotype of the rs3761847 SNP showed a tendency to associate with multiple brain parasites, while the CT and GG genotypes of the rs17611 and rs3761847 SNPs, respectively, showed a tendency to associate with low CSF cellularity. The rs3761847 SNP was associated with epilepsy under a dominant model, whereas rs10818488 was associated with CSF cellularity and parasite load under dominant and recessive models, respectively. For haplotypes, C5- and the TRAF1-associated SNPs were, respectively, in strong linkage disequilibrium with each other; thus, these haplotypes were studied independently. For C5 SNPs, carrying the CAA haplotype increases the risk of showing high CSF cellularity 3-fold and the risk of having extraparenchymal parasites 4-fold, two conditions that are related to severe disease. For TRAF1 SNPs, the GA and AG haplotypes were associated with CSF cellularity, and the AG haplotype was associated with epilepsy. Overall, these findings support the clear participation of C5 and TRAF1 in the risk of developing severe neurocysticercosis in the Mexican population.

Using detergent-enhanced LAMP for African trypanosome detection in human cerebrospinal fluid and implications for disease staging.

OBJECTIVE: Where human African trypanosomiasis (HAT) patients are seen, failure to microscopically diagnose infections by Trypanosoma brucei gambiense in blood smears and/or cerebrospinal fluid (CSF) in the critical early stages of the disease is the single most important factor in treatment failure, a result of delayed treatment onset or its absence. We hypothesized that the enhanced sensitivity of detergent-enhanced loop-mediated isothermal amplification (LAMP) will allow for point of care (POC) detection of African trypanosomes in the CSF of HAT patients where the probability for detecting a single parasite or parasite DNA molecule in 1 µL of CSF sample is negligible by current methods. METHODOLOGY: We used LAMP targeting the multicopy pan-T. brucei repetitive insertion mobile element (RIME LAMP) and the Trypanosoma brucei gambiense 5.8S rRNA-internal transcribed spacer 2 gene (TBG1 LAMP). We tested 1 µL out of 20 µL sham or Triton X-100 treated CSFs from 73 stage-1 and 77 stage-2 HAT patients from the Central African Republic and 100 CSF negative controls. RESULTS: Under sham conditions, parasite DNA was detected by RIME and TBG1 LAMP in 1.4% of the stage-1 and stage-2 gambiense HAT CSF samples tested. After sample incubation with detergent, the number of LAMP parasite positive stage-2 CSF's increased to 26%, a value which included the 2 of the 4 CSF samples where trypanosomes were identified microscopically. Unexpected was the 41% increase in parasite positive stage-1 CSF's detected by LAMP. Cohen's kappa coefficients for RIME versus TBG1 LAMP of 0.92 (95%CI: 0.82-1.00) for stage-1 and 0.90 (95%CI: 0.80-1.00) for stage-2 reflected a high level of agreement between the data sets indicating that the results were not due to amplicon contamination, data confirmed in χ2 tests (p<0.001) and Fisher's exact probability test (p = 4.7e-13). CONCLUSION: This study detected genomic trypanosome DNA in the CSF independent of the HAT stage and may be consistent with early CNS entry and other scenarios that identify critical knowledge gaps for future studies. Detergent-enhanced LAMP could be applicable for non-invasive African trypanosome detection in human skin and saliva or as an epidemiologic tool for the determination of human (or animal) African trypanosome prevalence in areas where chronically low parasitemias are present.

Primary amoebic meningoencephalitis in an infant.

Primary amoebic meningoencephalitis is rare but fatal disease encountered in immunocompetent individuals. Here, we present a case of a previously healthy 8-month-old female child, who presented with features of meningoencephalitis of 2 days' duration. Rapidly moving trophozoites of amoeba were observed in cerebrospinal fluid, which were confirmed to be Naegleria fowleri on polymerase chain reaction. Broad-spectrum antimicrobial therapy with ceftriaxone, vancomycin, amphotericin B and acyclovir was initiated. However, the patient deteriorated and left the hospital against medical advice. The isolation of N. fowleri in this case demands for increased awareness for prompt diagnosis and management in view of its high mortality.

Cerebral sparganosis presenting with atypical postcontrast magnetic resonance imaging findings: a case report and literature review.

BACKGROUND: Sparganosis, a rare and severe parasitic infection caused by the larvae of Spirometra species or simply sparganum, generally involves subcutaneous tissue or muscle. But occasionally, sparganum can also invade the human brain, resulting in cerebral sparganosis. CASE PRESENTATION: A 33-year-old woman presented with a 10-day history of headache. Postcontrast magnetic resonance imaging (MRI) revealed an irregular lesion with enhancement and the tunnel-shaped focus extending to the contralateral hemiphere. Cerebrospinal fluid (CSF) analysis disclosed pleocytosis (166 cells/µL) and an elevated protein concentration (0.742 g/L). Enzyme-linked immunosorbent assay (ELISA) revealed positive sparganum-specific antibody in both blood and CSF. Finally, the diagnosis of cerebral sparganosis was comfirmed. She received praziquantel treatment and got a favorable outcome during six-month follow-up. CONCLUSIONS: Irregular enhancement and the tunnel sign that extends to the contralateral hemisphere on postconstrast MRI are unusual presentations of cerebral sparganosis. ELISA for sparganum-specific antibody can help confirm the diagnosis. Although surgery is the preferred treatment for cerebral sparganosis, praziquantel might also achieve satisfying outcomes.

Surgical case of subacute headache in a young Latin American woman.

Neurocysticercosis (NCC) is the most common helmintic disease affecting the central nervous system and a major cause of adult-onset epilepsy in the developing world. 1 We describe a case of intraventricular NCC associated with hydrocephalus in a 28-year-old woman, Peruvian native, admitted to the emergency department for subacute headache and nausea. The cranial CT scan done showed asymmetric enlargement of the lateral ventricles which on cranial MRI was revealed to be due to an intraventricular cyst. An intraventricular endoscope was used to remove the cyst at the foramina of Monro, and therefore treat the obstructive hydrocephalus. NCC-a known cause of hydrocephalus in many Latin American countries-should be among the differential diagnosis in a patient with history of travel or residency in these countries. Treatment of choice for obstructive hydrocephalus caused by NCC is cyst removal with neuroendoscopy.

Melarsomine hydrochloride (Cymelarsan®) fails to cure horses with Trypanosoma equiperdum OVI parasites in their cerebrospinal fluid.

The aim of this study was to evaluate the ability of melarsomine hydrochloride (Cymelarsan®) to cure horses suffering from a nervous form of dourine, a sexually-transmitted disease caused by Trypanosoma equiperdum. The recently described experimental model for assessing drug efficacy against horse trypanosomosis allowed us to obtain eight horses (Welsh pony mares) infected by T. equiperdum with parasites in their cerebrospinal fluid. The Cymelarsan® treatment evaluated consisted of the daily administration of 0.5 mg/kg of Cymelarsan® over 7 days. Two control horses remained untreated, three horses received the treatment 36 days p.i. and three horses received the treatment 16 days p.i. Following treatment, we observed parasite clearance in blood, stabilization of rectal temperature and a relative improvement in the mean packed cell volume levels for all treated horses. However, live parasites were later observed again in the CSF of all treated horses. Our results indicate the inability of Cymelarsan® to reach Trypanozoon located in the central nervous system of infected horses and thus discourage the use of Cymelarsan® to treat animals suffering from a nervous form of dourine.

[Chagas disease affecting the central nervous system in a patient with AIDS demonstrated by quantitative molecular methods]. / Enfermedad de Chagas del sistema nervioso central en un paciente con SIDA demostrada por métodos cuantitativos moleculares.

Although infrequent, Trypanosoma cruzi reactivation is possible among patients with HIV/AIDS infection that develop a tumor-like or granulomatous lesion in the CNS. We report the case of a 60 years old male patient with HIV/AIDS and low CD4 lymphocytes count with cerebellar symptoms and mild paresis, associated to supra and infratentorial hypodense lesions and positive serology tests both to T. gondii and Trypanosoma cruzi. Empirical therapy against toxoplasmosis was prescribed together with antiretroviral therapy but without a favorable response. Brain Chagas disease was confirmed by quantitative PCR in the CSF but he died despite nifurtimox treatment. Despite its rare occurrence, Chagas disease affecting the CNS is possible among patients with HIV/AIDS infection. Epidemiological exposure, a positive Chagas serological test and the image pattern of brain lesions support the suspicion. Diagnosis can be confirmed by molecular test in CSF samples, including new quantitative methods. Despite an adverse prognosis, specific therapy can be attempted besides antiretroviral treatment.

Genotyping of Toxoplasma gondii strain directly from human CSF samples of congenital toxoplasmosis clinical case.

This report describes a case of congenital toxoplasmosis in a newborn in Southern Italy. A pregnant mother had been admitted at the 20th week of her pregnancy on account of pharyngodynia and laterocervical lymphadenopathy. Although serological testing of the mother's serum documented a seroconversion with positive IgG and IgM anti-Toxoplasma antibodies during II trimester, the woman refused to perform prenatal diagnosis for congenital toxoplasmosis. Fetal ultrasound scan already showed mild asymmetrical triventricular hydrocephaly and cerebral calcifications. After birth, real-time PCR on cerebrospinal fluid and blood samples of the newborn showed a positive result for 529bp-repeat element DNA of T. gondii, In addition brain magnetic resonance imaging and computed tomography showed a characteristic diffuse brain tissue loss associated with hydrocephalus. For the first time molecular characterization of T. gondii isolate was performed directly from the newborn's CSF samples by using nested-PCR-RFLP of sag-2 and pk1 genes. The PCR-RLFP analysis revealed that the isolate belongs to the clonal type II, the predominant lineage causing human toxoplasmosis, as confirmed by DNA sequencing.

Enfermedad de Chagas del sistema nervioso central en un paciente con SIDA demostrada por métodos cuantitativos moleculares / Chagas disease affecting the central nervous system in a patient with AIDS demonstrated by quantitative molecular methods

Although infrequent, Trypanosoma cruzi reactivation is possible among patients with HIV/AIDS infection that develop a tumor-like or granulomatous lesion in the CNS. We report the case of a 60 years old male patient with HIV/AIDS and low CD4 lymphocytes count with cerebellar symptoms and mild paresis, associated to supra and infratentorial hypodense lesions and positive serology tests both to T. gondii and Trypanosoma cruzi. Empirical therapy against toxoplasmosis was prescribed together with antiretroviral therapy but without a favorable response. Brain Chagas disease was confirmed by quantitative PCR in the CSF but he died despite nifurtimox treatment. Despite its rare occurrence, Chagas disease affecting the CNS is possible among patients with HIV/AIDS infection. Epidemiological exposure, a positive Chagas serological test and the image pattern of brain lesions support the suspicion. Diagnosis can be confirmed by molecular test in CSF samples, including new quantitative methods. Despite an adverse prognosis, specific therapy can be attempted besides antiretroviral treatment.

La reactivación de la infección por Trypanosoma cruzi es un diagnóstico infrecuente pero posible en pacientes con infección por VIH/SIDA y una lesión de tipo tumoral o granulomatosa en el sistema nervioso central. Presentamos el caso clínico de un paciente de 60 años con VIH/SIDA y recuentos bajos de linfocitos CD4, con síntomas cerebelosos y paresia leve, lesiones hipodensas supra e infratentoriales y serología positiva para Toxoplasma gondii y T. cruzi. Se trató empíricamente como una toxoplasmosis cerebral y con terapia antiretroviral, sin respuesta clínica. La enfermedad de Chagas cerebral se confirmó por RPC cuantitativa en el LCR. El paciente falleció a pesar de recibir terapia con nifurtimox. Apoyan la posibilidad de un Chagas cerebral en pacientes con VIH/SIDA, la exposición epidemiológica, la serología positiva y el patrón de distribución de las lesiones en las imágenes. El diagnóstico puede mejorarse con técnicas moleculares cuantitativas en LCR. A pesar de su mal pronóstico, se puede intentar una terapia específica junto al tratamiento antiretroviral.

Therapeutic apheresis using a mononuclear cell program to lower the microfilaria burden of a 23-year-old African woman with loiasis.

Apheresis has been used to lower the parasite burden of patients with Loa loa infection, but there are no reports regarding how to do this using modern, continuous flow equipment with a currently available program. A 23-year-old female refugee from Cameroon with known Loa loa infection presented to our Emergency Department with acute mental status changes and a picture of encephalitis. Lumbar puncture revealed Loa loa in her cerebrospinal fluid. Her midday blood microfilaria count was 15,000/mL. Because treatment with diethylcarbamazine was under consideration, we were asked to lower her parasite burden using apheresis. One single 2-total blood volume apheresis using the mononuclear cell program (without hydroxyethyl starch) on a COBE® Spectra Apheresis System decreased the microfilarial load from 15,000/mL to 10,666/mL, a 29% reduction. J. Clin. Apheresis 32:200-202, 2017. © 2016 Wiley Periodicals, Inc.