Haemophilus influenzae Meningitis Direct Diagnosis by Metagenomic Next-Generation Sequencing: A Case Report.
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ABSTRACT:
SUBMITTER: Morsli M
PROVIDER: S-EPMC8069228 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The current point-of-care diagnosis of enterovirus meningitis does not identify the viral genotype, which is prognostic. In this case report, more than 81% of an Echovirus 12 genome were detected and identified by metagenomic next-generation sequencing, directly from the cerebrospinal fluid collected in a 6-month-old child with meningeal syndrome and meningitis: introducing Echovirus 12 as an etiological agent of acute meningitis in the pediatric population.
| S-EPMC8156364 | biostudies-literature
Project description:BackgroundMycoplasma hominis meningitis is a rare postoperative complication of neurosurgery. Accurate and early diagnosis of M. hominis remains challenging because of the limitations of traditional detection methods. Metagenomic next-generation sequencing (mNGS) is an advanced technique with high sensitivity and specificity for identifying infectious pathogens; however, its application in diagnosing M. hominis meningitis has not been widely studied.Case presentationWe report the case of a 61-year-old man who presented with fever and headache after neurosurgical treatment for a cerebral hemorrhage. Empiric antibiotic therapy was ineffective. Traditional culture of pathogens and serological testing yielded negative results, but M. hominis was detected in the cerebrospinal fluid by mNGS. After further verification by polymerase chain reaction (PCR), the patient's clinical treatment was adjusted accordingly. With targeted antibiotic intervention, the patient's symptoms were effectively alleviated, and clinical indicators returned to normal levels. Furthermore, the abundance of M. hominis decreased significantly compared to the initial mNGS reading after targeted treatment, indicating that the infection caused by M. hominis was effectively controlled.ConclusionUsing mNGS, we found that M. hominis may be a candidate causative agent of meningitis. The technique also has the advantage of timeliness and accuracy that traditional cultures cannot achieve. A combination of mNGS with PCR is recommended to identify pathogens in the early stages of infectious diseases to administer targeted clinical medication.
| S-EPMC9380824 | biostudies-literature
Project description:Abstract Background Metagenomic next-generation sequencing (mNGS) of CSF can identify nearly all pathogens in a single test. We previously validated a CSF mNGS assay in a licensed clinical laboratory. To date, the utility of mNGS for infectious disease diagnosis has been described in case reports and small case series, but not in a large-scale clinical trial. Methods The PDAID (“Precision Diagnosis of Acute Infectious Diseases”) study was a 1-year nationwide prospective study across 8 tertiary care hospitals to evaluate the performance and utility of a clinical metagenomic sequencing assay for diagnosis of meningitis, encephalitis, or myelitis from cerebrospinal fluid (CSF) (ClinicalTrials.gov number NCT02910037). We recruited acutely ill hospitalized inpatients lacking a diagnosis at the time of enrollment. CSF samples were processed and analyzed by mNGS testing within 1 week of receipt in the clinical microbiology laboratory, with sequencing results reported in the patient medical record and used to make contemporaneous treatment decisions. Weekly clinical microbial sequencing boards were convened to discuss mNGS results with treating physicians, and clinical impact evaluated by surveys, chart review, and direct clinician feedback. Results A total of 204 patients were enrolled. Patients were severely ill (ICU 48%, average length of stay 26 days, overall 30-day mortality 7.4%). Fifty-nine neurologic infections were diagnosed in 57 patients (27.9%). mNGS identified 15 (25.4%) infections that were missed by all conventional microbiological tests, including emerging and/or uncommon pathogens such as St. Louis encephalitis virus, hepatitis E virus acquired by lung transplant, and Nocardia farcinica. Twelve of the 15 mNGS-only diagnoses (80%) had clinical impact, with 9 of 15 (60%) guiding appropriate treatment. For diagnosis of infections by direct detection CSF testing, mNGS had 79.1% sensitivity and 98.8% specificity, versus 65.1% sensitivity and 99.4% specificity by conventional testing. Conclusion A significant proportion of neurologic infections are missed despite extensive diagnostic testing performed in tertiary care hospitals. Clinical metagenomic CSF testing was found to be useful in increasing the number of diagnosed neurologic infections and providing actionable information for physicians. Disclosures All authors: No reported disclosures.
| S-EPMC6252609 | biostudies-literature
Project description:Importance:Identifying infectious causes of subacute or chronic meningitis can be challenging. Enhanced, unbiased diagnostic approaches are needed. Objective:To present a case series of patients with diagnostically challenging subacute or chronic meningitis using metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) supported by a statistical framework generated from mNGS of control samples from the environment and from patients who were noninfectious. Design, Setting, and Participants:In this case series, mNGS data obtained from the CSF of 94 patients with noninfectious neuroinflammatory disorders and from 24 water and reagent control samples were used to develop and implement a weighted scoring metric based on z scores at the species and genus levels for both nucleotide and protein alignments to prioritize and rank the mNGS results. Total RNA was extracted for mNGS from the CSF of 7 participants with subacute or chronic meningitis who were recruited between September 2013 and March 2017 as part of a multicenter study of mNGS pathogen discovery among patients with suspected neuroinflammatory conditions. The neurologic infections identified by mNGS in these 7 participants represented a diverse array of pathogens. The patients were referred from the University of California, San Francisco Medical Center (n = 2), Zuckerberg San Francisco General Hospital and Trauma Center (n = 2), Cleveland Clinic (n = 1), University of Washington (n = 1), and Kaiser Permanente (n = 1). A weighted z score was used to filter out environmental contaminants and facilitate efficient data triage and analysis. Main Outcomes and Measures:Pathogens identified by mNGS and the ability of a statistical model to prioritize, rank, and simplify mNGS results. Results:The 7 participants ranged in age from 10 to 55 years, and 3 (43%) were female. A parasitic worm (Taenia solium, in 2 participants), a virus (HIV-1), and 4 fungi (Cryptococcus neoformans, Aspergillus oryzae, Histoplasma capsulatum, and Candida dubliniensis) were identified among the 7 participants by using mNGS. Evaluating mNGS data with a weighted z score-based scoring algorithm reduced the reported microbial taxa by a mean of 87% (range, 41%-99%) when taxa with a combined score of 0 or less were removed, effectively separating bona fide pathogen sequences from spurious environmental sequences so that, in each case, the causative pathogen was found within the top 2 scoring microbes identified using the algorithm. Conclusions and Relevance:Diverse microbial pathogens were identified by mNGS in the CSF of patients with diagnostically challenging subacute or chronic meningitis, including a case of subarachnoid neurocysticercosis that defied diagnosis for 1 year, the first reported case of CNS vasculitis caused by Aspergillus oryzae, and the fourth reported case of C dubliniensis meningitis. Prioritizing metagenomic data with a scoring algorithm greatly clarified data interpretation and highlighted the problem of attributing biological significance to organisms present in control samples used for metagenomic sequencing studies.
| S-EPMC5933460 | biostudies-literature
Project description:Whole genome sequencing direct diagnosis of Haemophilus influenzae meningitis: a case report.
| PRJEB41765 | ENA
Project description:Whole genome sequencing direct diagnosis of Haemophilus influenzae meningitis: a case report.
| PRJEB41766 | ENA
Project description:Haemophilus influenzae meningitis direct diagnosis by whole genome sequencing: a case report.
| PRJEB41704 | ENA
Project description:BackgroundTuberculous meningitis (TBM) is a severe form of extrapulmonary tuberculosis and its early diagnosis is very difficult leading to present with severe disability or die. The current study aimed to assess the accuracy of metagenomic next generation sequencing (mNGS) for TBM, and to identify a new test for the early diagnosis of TBM.MethodsWe searched for articles published in Embase, PubMed, Cochrane Library, China National Knowledge Infrastructure, and Wanfang Data up to June 30, 2020 for studies that assessed the efficacy of mNGS for the diagnosis of TBM. Then, the accuracy between mNGS and a composite reference standard (CRS) in these articles was compared using the meta-analysis approach.ResultsFour independent studies with 342 samples comparing mNGS and a CRS were included in this study. The sensitivity of mNGS for TBM diagnosis ranged from 27% to 84%. The combined sensitivity of mNGS was 61%, and the I2 value was 92%. Moreover, the specificity of mNGS for TBM diagnosis ranged from 96% to 100%. The combined specificity of mNGS was 98%, and the I2 value was 74%. The heterogeneity between studies in terms of sensitivity and specificity was significant. The area under the curve (AUC) of the summary receiver operating characteristic curve (SROC) of mNGS for TBM was 0.98.ConclusionsThe sensitivity of mNGS for TBM diagnosis was moderate. Furthermore, the specificity was extremely high, and the AUC of the SROC indicated a very good diagnostic efficacy. mNGS could be used as an early diagnostic method for TBM, however, the results should be treated with caution for the heterogeneity between studies was extremely significant.Systematic review registrationINPLASY202070100.
| S-EPMC7707562 | biostudies-literature
Project description:Cat-scratch disease (CSD) is an anthropozoonotic infection caused by Bartonella henselae, and it is one of the most common causes of lymph node infections in children and adolescents. B. henselae, belonging to the genus Bartonella, is a common human pathogen of human beings. CSD commonly develops as a result of cat scratches and bites or when injured skin comes into contact with cat saliva. The manifestation of CSD clinically differs for each patient based on their immune system. Individuals who have healthy immune systems generally manifest minimal clinical symptoms and do not necessitate any form of treatment. However, patients who have hypo-immunity require prompt medical attention due to the potential manifestation of severe symptoms that affect multiple systems of the body. Long latency and atypical clinical manifestations are characteristics of CSD. Bartonella isolation and identification are challenging procedures that require specialized equipment. There is no gold standard method for CSD diagnosis, and misdiagnosis and missed diagnosis rates are typically high. We present the case of a middle-aged male patient who developed fever, chills, anal distension, dizziness, and muscle pain for 10 days. The patient had a documented history of cat bites 1 month prior to the onset of symptoms. Following admission, he underwent an examination to determine superficial lymphadenopathy and hypoimmunity. Additionally, he had a fever during the disease. As the patient refused a needle biopsy of lymph nodes, metagenomic next-generation sequencing (mNGS) was employed and B. henselae was detected in the peripheral blood. The patient was diagnosed with CSD and treated with a combination of azithromycin and doxycycline. The fever symptoms were alleviated, and the patient was ultimately discharged. As a result of this case, we suggest that mNGS be used as a crucial supplementary diagnostic tool for individuals with compromised immune systems who may have CSD, especially when conventional diagnostic methods are inconclusive.
| S-EPMC10822884 | biostudies-literature
Project description:Background: Talaromycosis is a serious fungal infection which is rare in immunocompetent people. Since its clinical manifestations lack specificity, it is easy to escape diagnosis or be misdiagnosed leading to high mortality and poor prognosis. It is necessary to be alert to the disease when broad-spectrum antibiotics do not work well in immunocompetent patients. Case Presentation: A 79-year-old man was admitted to our Infectious Diseases Department for recurrent fever and cough. Before admission he has been treated with piperacillin-tazobactam, moxifloxacin followed by antituberculous agents in other hospitals while his symptoms were not thoroughly eased. During the first hospitalization in another hospital, he has been ordered a series of examination including radionuclide whole body bone imaging, transbronchial needle aspiration for subcarinal nodes. However, the results were negative showing no neoplasm. After being admitted to our hospital, he underwent various routine examinations. The initial diagnosis was bacterial pneumonia, and he was given meropenem injection and tigecycline injection successively, but there were no improvement of symptoms and inflammatory indicators. In the end, the main pathogen Talaromyces marneffei was confirmed using Metagenomic Next-Generation Sequencing (mNGS), and his clinical symptoms gradually relieved after targeted antifungal treatment using voriconazole. Conclusion: When empirical anti-infective treatment is ineffective, it is necessary to consider the possibility of opportunistic fungal infections on immunocompetent patients. mNGS, as a new generation of pathogenic testing methods, can often detect pathogenic bacteria faster than traditional methods, providing important help for clinical decision-making.
| S-EPMC8039304 | biostudies-literature