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Azad MA, Patel R. Practical Guidance for Clinical Microbiology Laboratories: Microbiologic diagnosis of implant-associated infections. Clin Microbiol Rev 2024; 37:e0010423. [PMID: 38506553 DOI: 10.1128/cmr.00104-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
SUMMARYImplant-associated infections (IAIs) pose serious threats to patients and can be associated with significant morbidity and mortality. These infections may be difficult to diagnose due, in part, to biofilm formation on device surfaces, and because even when microbes are found, their clinical significance may be unclear. Despite recent advances in laboratory testing, IAIs remain a diagnostic challenge. From a therapeutic standpoint, many IAIs currently require device removal and prolonged courses of antimicrobial therapy to effect a cure. Therefore, making an accurate diagnosis, defining both the presence of infection and the involved microorganisms, is paramount. The sensitivity of standard microbial culture for IAI diagnosis varies depending on the type of IAI, the specimen analyzed, and the culture technique(s) used. Although IAI-specific culture-based diagnostics have been described, the challenge of culture-negative IAIs remains. Given this, molecular assays, including both nucleic acid amplification tests and next-generation sequencing-based assays, have been used. In this review, an overview of these challenging infections is presented, as well as an approach to their diagnosis from a microbiologic perspective.
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Affiliation(s)
- Marisa Ann Azad
- Division of Infectious Diseases, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canada
| | - Robin Patel
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Kommedal Ø, Eagan TM, Fløtten Ø, Leegaard TM, Siljan W, Fardal H, Bø B, Grøvan F, Larssen KW, Kildahl-Andersen A, Hjetland R, Tilseth R, Hareide SKØ, Tellevik M, Dyrhovden R. Microbiological diagnosis of pleural infections: a comparative evaluation of a novel syndromic real-time PCR panel. Microbiol Spectr 2024; 12:e0351023. [PMID: 38656204 DOI: 10.1128/spectrum.03510-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/19/2024] [Indexed: 04/26/2024] Open
Abstract
Current microbial diagnostics for pleural infections are insufficient. Studies using 16S targeted next-generation sequencing report that only 10%-16% of bacteria present are cultured and that 50%-78% of pleural fluids containing relevant microbial DNA remain culture negative. As a rapid diagnostic alternative suitable for clinical laboratories, we wanted to explore a PCR-based approach. Based on the identification of key pathogens, we developed a syndromic PCR panel for community-acquired pleural infections (CAPIs). This was a pragmatic PCR panel, meaning that it was not designed for detecting all possibly involved bacterial species but for confirming the diagnosis of CAPI, and for detecting bacteria that might influence choice of antimicrobial treatment. We evaluated the PCR panel on 109 confirmed CAPIs previously characterized using culture and 16S targeted next-generation sequencing. The PCR secured the diagnosis of CAPI in 107/109 (98.2%) and detected all present pathogens in 69/109 (63.3%). Culture secured the diagnosis in 54/109 (49.5%) and detected all pathogens in 31/109 (28.4%). Corresponding results for 16S targeted next-generation sequencing were 109/109 (100%) and 98/109 (89.9%). For bacterial species included in the PCR panel, PCR had a sensitivity of 99.5% (184/185), culture of 21.6% (40/185), and 16S targeted next-generation sequencing of 92.4% (171/185). None of the bacterial species present not covered by the PCR panel were judged to impact antimicrobial therapy. A syndromic PCR panel represents a rapid and sensitive alternative to current diagnostic approaches for the microbiological diagnosis of CAPI.IMPORTANCEPleural empyema is a severe infection with high mortality and increasing incidence. Long hospital admissions and long courses of antimicrobial treatment drive healthcare and ecological costs. Current methods for microbiological diagnostics of pleural infections are inadequate. Recent studies using 16S targeted next-generation sequencing as a reference standard find culture to recover only 10%-16% of bacteria present and that 50%-78% of samples containing relevant bacterial DNA remain culture negative. To confirm the diagnosis of pleural infection and define optimal antimicrobial therapy while limiting unnecessary use of broad-spectrum antibiotics, there is a need for rapid and sensitive diagnostic approaches. PCR is a rapid method well suited for clinical laboratories. In this paper we show that a novel syndromic PCR panel can secure the diagnosis of pleural infection and detect all bacteria relevant for choice of antimicrobial treatment with a high sensitivity.
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Affiliation(s)
- Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Tomas Mikal Eagan
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Øystein Fløtten
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Truls Michael Leegaard
- Division of Medicine and Laboratory Sciences, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Akershus, Norway
| | - William Siljan
- Department of Pulmonary Medicine, Akershus University Hospital, Lorenskog, Akershus, Norway
| | - Hilde Fardal
- Department of Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Bjørnar Bø
- Department of Pulmonary Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Fredrik Grøvan
- Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Kjersti Wik Larssen
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Arne Kildahl-Andersen
- Department of Thoracic Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Reidar Hjetland
- Department of Microbiology, Førde Central Hospital, Førde, Norway
| | - Rune Tilseth
- Department of Medicine, Førde Central Hospital, Førde, Norway
| | | | - Marit Tellevik
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Ruben Dyrhovden
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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Al Nuaimi M, Al Khaaldi A, Trad O, Almulla A, Al Rufaye H, Ghatasheh G, Al Dhaheri F. HHV6-Associated Hydrocephalus in a Pediatric Hematopoietic Stem Cell Transplant Recipient: An Unusual Presentation. J Pediatr Hematol Oncol 2024:00043426-990000000-00427. [PMID: 38832402 DOI: 10.1097/mph.0000000000002892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/25/2024] [Indexed: 06/05/2024]
Abstract
Human herpesvirus 6 (HHV-6) is a widely spread DNA virus that is ubiquitous and persistent with primary infection occurring in early childhood, with reactivation of the infection a common phenomenon in severely immunocompromised hosts, including hematopoietic stem cell transplant (HSCT) patients, influencing morbidity and mortality. A wide spectrum of clinical presentations is reported in the literature with HHV-6 reactivation including post-transplant limbic encephalitis (PALE). We report the unusual case of a 6-year-old female 107 days postallogenic HSCT due to transfusion dependent beta thalassemia major who developed acute cerebellitis with secondary supratentorial hydrocephalus that required invasive surgical intervention. In addition to accompanying imaging findings, the patient tested positive for HHV-6 by PCR from both serum and CSF samples and demonstrated dramatic improvement with the institution of steroid therapy in addition to ganciclovir treatment. The availability of rapid diagnostic measures in addition to a multidisciplinary approach is crucial to manage HHV-6 encephalitis and associated complications in HSCT patients.
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Affiliation(s)
- Mohammed Al Nuaimi
- Division of Pediatric Hematology and Oncology, Tawam Oncology Centre
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain
| | - Aisha Al Khaaldi
- Department of Pediatrics, Al Qassimi Women and Children Hospital
- Sharjah University Hospital, Sharjah
| | - Omar Trad
- Division of Pediatric Hematology and Oncology, Tawam Oncology Centre
| | - Asia Almulla
- Division of Pediatric Hematology and Oncology, Tawam Oncology Centre
- Sharjah University Hospital, Sharjah
| | - Haydar Al Rufaye
- Division of Pediatric Hematology and Oncology, Tawam Oncology Centre
| | - Ghassan Ghatasheh
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Tawam Hospital
| | - Fatima Al Dhaheri
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain
- Pediatric Infectious Diseases Unit, Department of Pediatrics, Sheikh Khalifa Medical City, Abu-Dhabi, United Arab Emirates
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O'Meara KT, Chan JL, Ceron S, Lam JC. Polymerase chain reaction negative cryptococcal meningitis. Diagn Microbiol Infect Dis 2024; 109:116251. [PMID: 38492489 DOI: 10.1016/j.diagmicrobio.2024.116251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 03/07/2024] [Indexed: 03/18/2024]
Abstract
A 61-year-old male with subacute headache was found to have cryptococcal meningitis despite a negative BioFire FilmArray meningitis/encephalitis panel. This case underscores the importance of liberal cryptococcal antigen testing, and that a negative FilmArray panel is inadequate in excluding cryptococcal meningitis, particularly in a HIV-negative host.
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Affiliation(s)
- Kyle T O'Meara
- Department of Pulmonary & Critical Care, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - June L Chan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Stacey Ceron
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - John C Lam
- Division of Infectious Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States.
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Gupta C, Dogra P, Jain V, Kaur R, Sharma JB. HIV-associated disseminated cryptococcosis-An unusual clinical and diagnostic picture with successful cure by single dose liposomal amphotericin B treatment. Diagn Microbiol Infect Dis 2024; 109:116217. [PMID: 38513558 DOI: 10.1016/j.diagmicrobio.2024.116217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Cryptococcosis is an invasive, opportunistic fungal infection seen especially in human immunodeficiency virus (HIV) infected patients. Cryptococcal meningitis (CM) is the second leading cause of mortality in HIV patients. We report a case of disseminated cryptococcosis presenting with altered mental status in a newly diagnosed HIV infection. METHODS AND RESULTS A 50-year-old with a short history of altered mental sensorium and a history of low-grade fever and weight loss for few months presented at a tertiary care hospital in North India. He was detected positive for HIV-1. Cryptococcal antigen (CRAG) was positive in Cerebrospinal fluid (CSF), and negative in serum. The fungal culture in CSF was sterile while the fungal blood culture grew Cryptococcus neoformans. The patient was treated with single high-dose Liposomal Amphotericin B (LAmB) therapy followed by Fluconazole and Flucytosine for the next two weeks followed by fluconazole daily for consolidation and maintenance therapy. Antiretroviral therapy (ART) was started 4 weeks after induction therapy. After 6 months, the patient is doing fine. CONCLUSION Single dose LAmB along with the backbone of fluconazole and flucytosine appears promising in disseminated cryptococcal infection in HIV-infected individuals.
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Affiliation(s)
- Chhavi Gupta
- Infectious disease, Yashoda Superpseciality Hospital, Kaushambi, India.
| | | | - Varun Jain
- Neuroanaesthesia and Critical Care, Fortis Hospital, Noida, India
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Launes C, Camacho J, Pons-Espinal M, López-Labrador FX, Esteva C, Cabrerizo M, Fernández-García MD, Fogeda M, Masa-Calles J, López-Perea N, Echevarría JE, Muñoz-Almagro C, Tarragó D. Hybrid capture shotgun sequencing detected unexpected viruses in the cerebrospinal fluid of children with acute meningitis and encephalitis. Eur J Clin Microbiol Infect Dis 2024; 43:863-873. [PMID: 38438704 PMCID: PMC11108891 DOI: 10.1007/s10096-024-04795-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/26/2024] [Indexed: 03/06/2024]
Abstract
PURPOSE Investigation of undiagnosed cases of infectious neurological diseases, especially in the paediatric population, remains a challenge. This study aimed to enhance understanding of viruses in CSF from children with clinically diagnosed meningitis and/or encephalitis (M/ME) of unknown aetiology using shotgun sequencing enhanced by hybrid capture (HCSS). METHODS A single-centre prospective study was conducted at Sant Joan de Déu University Hospital, Barcelona, involving 40 M/ME episodes of unknown aetiology, recruited from May 2021 to July 2022. All participants had previously tested negative with the FilmArray Meningitis/Encephalitis Panel. HCSS was used to detect viral nucleic acid in the patients' CSF. Sequencing was performed on Illumina NovaSeq platform. Raw sequence data were analysed using CZ ID metagenomics and PikaVirus bioinformatics pipelines. RESULTS Forty episodes of M/ME of unknown aetiology in 39 children were analysed by HCSS. A significant viral detection in 30 CSF samples was obtained, including six parechovirus A, three enterovirus ACD, four polyomavirus 5, three HHV-7, two BKV, one HSV-1, one VZV, two CMV, one EBV, one influenza A virus, one rhinovirus, and 13 HERV-K113 detections. Of these, one sample with BKV, three with HHV-7, one with EBV, and all HERV-K113 were confirmed by specific PCR. The requirement for Intensive Care Unit admission was associated with HCSS detections. CONCLUSION This study highlights HCSS as a powerful tool for the investigation of undiagnosed cases of M/ME. Data generated must be carefully analysed and reasonable precautions must be taken before establishing association of clinical features with unexpected or novel virus findings.
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Affiliation(s)
- Cristian Launes
- Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Departament de Medicina i Especialitats Medicoquirúrgiques, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Juan Camacho
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda- Pozuelo km 2, 28220, Majadahonda, Spain
| | - Marina Pons-Espinal
- Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - F Xavier López-Labrador
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Genomics & Health Department, FISABIO-Public Health Foundation, Valencia, Spain
- Department of Microbiology and Ecology, Medical School, University of Valencia, Valencia, Spain
| | - Cristina Esteva
- Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - María Cabrerizo
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda- Pozuelo km 2, 28220, Majadahonda, Spain
| | - María Dolores Fernández-García
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda- Pozuelo km 2, 28220, Majadahonda, Spain
| | | | - Josefa Masa-Calles
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Avda Monforte de Lemos 5, Madrid, Spain
| | - Noemí López-Perea
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Avda Monforte de Lemos 5, Madrid, Spain
| | - Juan Emilio Echevarría
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda- Pozuelo km 2, 28220, Majadahonda, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - David Tarragó
- CIBER Epidemiology and Public Health (CIBERESP), Madrid, Spain.
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda- Pozuelo km 2, 28220, Majadahonda, Spain.
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Erba A, Franzeck FC, Hinic V, Egli A, Osthoff M. Utilization of a Meningitis/Encephalitis PCR panel at the University Hospital Basel - a retrospective study to develop a diagnostic decision rule. Front Med (Lausanne) 2024; 11:1351903. [PMID: 38695026 PMCID: PMC11061443 DOI: 10.3389/fmed.2024.1351903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/05/2024] [Indexed: 05/04/2024] Open
Abstract
Background The Biofire® FilmArray® Meningitis/Encephalitis (ME) PCR panel covers 14 viral, bacterial, and fungal pathogens and has been implemented in many institutions worldwide. Post-marketing studies indicate a reduced sensitivity and overutilization underscoring the need for a more targeted usage. The aim of our study is to describe the utilization of the ME panel and to develop a diagnostic-stewardship based decision rule. Materials Adult patients, who underwent CSF analysis with the ME panel between August 2016 and June 2021 at the University Hospital Basel, were included. Demographic, clinical, microbiological, and laboratory data were extracted from the electronic health record. Factors associated with a positive ME panel result were identified, and a decision rule was developed to potentially optimize the diagnostic yield and reduce the number of unnecessary tests. Results 1,236 adult patients received at least one panel in the observed period, of whom 106 panels tested positive (8.6%). The most frequently observed pathogens were Varicella Zoster Virus (VZV, 27%), Streptococcus pneumoniae (19%), Enterovirus (16%), Herpes simplex Virus 1/2 (16%), and Human Herpesvirus 6 (HHV-6, 13%). Fever, vomiting, headache, and photophobia were more frequently present in test positive patients as were significantly higher CSF leukocytes and protein concentrations. When simulating a decision rule based on CSF leukocytes and protein concentration, only 35% of all patients would have qualified for a ME panel tests, thereby increasing the positivity rate to 22.7%. 10 of 106 positive ME panels would have been missed, only involving HHV-6 and VZV (6 and 4 cases, respectively). As these subjects were either severely immunocompromised or had clinical features of shingles we propose extending the testing algorithm by including those criteria. Conclusion The ME panel positivity rate at our institution was similar as previously published. Our results highlight the need for diagnostic-stewardship interventions when utilizing this assay by implementing a stepwise approach based on a limited number of clinical and laboratory features. This decision rule may improve the pretest probability of a positive test result, increase the quality of test utilization, and reduce costs.
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Affiliation(s)
- Andrea Erba
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Fabian C. Franzeck
- Clinical Data Warehouse, Research and Analytics Services, University Hospital Basel, Basel, Switzerland
| | - Vladimira Hinic
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Michael Osthoff
- Department of Internal Medicine, University Hospital Basel, Basel, Switzerland
- Department of Internal Medicine, Cantonal Hospital Winterthur, Winterthur, Switzerland
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Cuesta G, Puerta-Alcalde P, Vergara A, Roses E, Bosch J, Casals-Pascual C, Soriano A, Marcos MÁ, Sanz S, Vila J. An Assessment of a New Rapid Multiplex PCR Assay for the Diagnosis of Meningoencephalitis. Diagnostics (Basel) 2024; 14:802. [PMID: 38667448 PMCID: PMC11048994 DOI: 10.3390/diagnostics14080802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
The rapid and broad microbiological diagnosis of meningoencephalitis (ME) has been possible thanks to the development of multiplex PCR tests applied to cerebrospinal fluid (CSF). We aimed to assess a new multiplex PCR panel (the QIAstat-Dx ME panel), which we compared to conventional diagnostic tools and the Biofire FilmArray ME Panel. The pathogens analyzed using both methods were Escherichia coli K1, Haemophilus influenzae, Listeria monocytogenes, Neisseria meningitidis, Streptococcus agalactiae, Streptococcus pneumoniae, Enterovirus, herpes simplex virus 1-2, human herpesvirus 6, human parechovirus, varicella zoster virus, and Cryptococcus neoformans/gattii. We used sensitivity, specificity, PPV, NPV, and kappa correlation index parameters to achieve our objective. Fifty CSF samples from patients with suspected ME were included. When conventional methods were used, 28 CSF samples (56%) were positive. The sensitivity and specificity for QIAstat-Dx/ME were 96.43% (CI95%, 79.8-99.8) and 95.24% (75.2-99.7), respectively, whereas the PPV and NPV were 96.43% (79.8-99.8) and 95.24% (75.1-99.7), respectively. The kappa value was 91.67%. Conclusions: A high correlation of the QIAstat-Dx ME panel with reference methods was shown. QIAstat-Dx ME is a rapid-PCR technique to be applied in patients with suspected ME with a high accuracy.
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Affiliation(s)
- Genoveva Cuesta
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain; (G.C.); (A.V.); (J.B.); (M.Á.M.)
| | - Pedro Puerta-Alcalde
- Department of Infectious Diseases, Hospital Clínic-IDIBAPS, University of Barcelona, 08007 Barcelona, Spain (A.S.)
| | - Andrea Vergara
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain; (G.C.); (A.V.); (J.B.); (M.Á.M.)
- Department of Basic Clinical Practice, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain;
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
| | - Enric Roses
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain; (G.C.); (A.V.); (J.B.); (M.Á.M.)
| | - Jordi Bosch
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain; (G.C.); (A.V.); (J.B.); (M.Á.M.)
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
| | - Climent Casals-Pascual
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain; (G.C.); (A.V.); (J.B.); (M.Á.M.)
- Department of Basic Clinical Practice, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain;
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
| | - Alex Soriano
- Department of Infectious Diseases, Hospital Clínic-IDIBAPS, University of Barcelona, 08007 Barcelona, Spain (A.S.)
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Mª Ángeles Marcos
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain; (G.C.); (A.V.); (J.B.); (M.Á.M.)
- Department of Basic Clinical Practice, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain;
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
| | - Sergi Sanz
- Department of Basic Clinical Practice, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain;
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jordi Vila
- Department of Clinical Microbiology, Hospital Clinic, 08036 Barcelona, Spain; (G.C.); (A.V.); (J.B.); (M.Á.M.)
- Department of Basic Clinical Practice, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain;
- CIBER Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institute of Global Health of Barcelona (ISGlobal), 08036 Barcelona, Spain
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Kadambari S, Feng S, Liu X, Andersson M, Waterfield R, Fodder H, Jacquemot A, Galal U, Rafferty A, Drew RJ, Rodrigues C, Sadarangani M, Riordan A, Martin NG, Defres S, Solomon T, Pollard AJ, Paulus S. Evaluating the Impact of the BioFire FilmArray in Childhood Meningitis: An Observational Cohort Study. Pediatr Infect Dis J 2024; 43:345-349. [PMID: 38190645 DOI: 10.1097/inf.0000000000004236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
BACKGROUND Multiplex polymerase chain reaction assays have the potential to reduce antibiotic use and shorten length of inpatient stay in children with suspected central nervous system infection by obtaining an early microbiological diagnosis. The clinical impact of the implementation of the BioFire FilmArray Meningitis/Encephalitis Panel on the management of childhood meningitis was evaluated at the John Radcliffe Hospital in Oxford and Children's Health Ireland at Temple Street in Dublin. METHODS Children who had lumbar punctures performed as part of a septic screen were identified retrospectively through clinical discharge coding and microbiology databases from April 2017 to December 2018. Anonymized clinical and laboratory data were collected. Comparison of antibiotic use, length of stay and outcome at discharge was made with a historical cohort in Oxford (2012-2016), presenting before implementation of the FilmArray. RESULTS The study included 460 children who had a lumbar puncture as part of an evaluation for suspected central nervous system infection. Twelve bacterial cases were identified on the FilmArray that were not detected by conventional bacterial culture. Bacterial culture identified one additional case of bacterial meningitis, caused by Escherichia coli , which had not been identified on the FilmArray. Duration of antibiotics was shorter in children when FilmArray was used than before its implementation; enterovirus meningitis (median: 4 vs. 5 days), human parechovirus meningitis (median: 4 vs. 4.5 days) and culture/FilmArray-negative cerebrospinal fluid (median: 4 vs. 6 days). CONCLUSIONS The use of a FilmArray can identify additional bacterial cases of meningitis in children that had been negative by traditional culture methods. Children with viral meningitis and culture-negative meningitis received shorter courses of antibiotics and had shorter hospital stays when FilmArray was used. Large studies to evaluate the clinical impact and cost effectiveness of incorporating the FilmArray into routine testing are warranted.
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Affiliation(s)
- Seilesh Kadambari
- From the Oxford Vaccine Group, Department of Paediatrics, University of Oxford, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
- Department of Paediatric Infectious Diseases, Great Ormond Street Hospital for Children NHS Foundation Trust
- Infection, Immunity and Inflammation department, University College London, Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Shuo Feng
- From the Oxford Vaccine Group, Department of Paediatrics, University of Oxford, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Xinxue Liu
- From the Oxford Vaccine Group, Department of Paediatrics, University of Oxford, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Monique Andersson
- Department of Microbiology, Oxford University Hospitals NHS Foundation Trust
- NDCLS, Radcliffe Department of Medicine
| | - Rebecca Waterfield
- From the Oxford Vaccine Group, Department of Paediatrics, University of Oxford, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Harriet Fodder
- From the Oxford Vaccine Group, Department of Paediatrics, University of Oxford, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Aimee Jacquemot
- From the Oxford Vaccine Group, Department of Paediatrics, University of Oxford, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Ushma Galal
- Oxford Primary Care Clinical Trials Unit, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | | | - Richard J Drew
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland at Temple Street
- Clinical Innovation Unit, Rotunda Hospital
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Republic of Ireland
| | - Charlene Rodrigues
- Department of Paediatric Infectious Diseases, St Mary's Hospital, Imperial College Healthcare NHS Trust
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Riordan
- Department of Paediatric Infectious Diseases and Immunology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Natalie G Martin
- Department of Paediatrics, University of Otago Christchurch, Christchurch, New Zealand
| | - Sylviane Defres
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Tropical and Infectious Diseases Unit, Liverpool University Hospitals NHS Foundation Trust
- Department of Clinical Sciences and Education, Liverpool School of Tropical Medicine
| | - Tom Solomon
- The Pandemic Institute
- Department of Clinical Infection, Microbiology, and Immunology (CIMI)
- Institute of Infection, Veterinary & Ecological Sciences
- National Institute for Health and Care Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool
- Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Andrew J Pollard
- From the Oxford Vaccine Group, Department of Paediatrics, University of Oxford, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Stephane Paulus
- From the Oxford Vaccine Group, Department of Paediatrics, University of Oxford, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
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10
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Hong YJ, Jung BK, Kim JK. Epidemiological Characterization of Respiratory Pathogens Using the Multiplex PCR FilmArray™ Respiratory Panel. Diagnostics (Basel) 2024; 14:734. [PMID: 38611647 PMCID: PMC11011807 DOI: 10.3390/diagnostics14070734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Various pathogens can cause upper respiratory tract infections, presenting challenges in accurate diagnosis due to similar symptomatology. Therefore, rapid and precise diagnostic tests are crucial for effective treatment planning. Traditional culture-based methods for diagnosis are limited by their reliance on skilled personnel and lengthy processing times. In contrast, multiplex polymerase chain reaction (PCR) techniques offer enhanced accuracy and speed in identifying respiratory pathogens. In this study, we aimed to assess the efficacy of the FilmArray™ Respiratory Panel (RP), a multiplex PCR test capable of simultaneously screening 20 pathogens. This retrospective analysis was conducted at Dankook University Hospital, South Korea, between January 2018 and December 2022. Samples from patients with upper respiratory tract infections were analyzed. Results revealed adenovirus as the most prevalent pathogen (18.9%), followed by influenza virus A (16.5%), among others. Notably, a 22.5% co-infection rate was observed. The FilmArray™ RP method successfully identified 20 pathogens within 2 h, facilitating prompt treatment decisions and mitigating unnecessary antibiotic prescriptions. This study underscores the utility of multiplex PCR in respiratory pathogen identification, offering valuable insights for epidemiological surveillance and diagnosis.
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Affiliation(s)
- Young Jun Hong
- Department of Biomedical Laboratory Science, College of Health Sciences, Dankook University, Cheonan 31116, Republic of Korea;
| | - Bo Kyeung Jung
- Department of Laboratory Medicine, College of Medicine, Dankook University, Cheonan 31116, Republic of Korea;
| | - Jae Kyung Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Dankook University, Cheonan 31116, Republic of Korea;
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11
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Matsuura H, Arimoto K, Takahashi Y, Kishimoto M. Combination of a multiplex pneumonia panel and Gram staining for antimicrobial selection to treat lower respiratory tract infection. Pneumonia (Nathan) 2024; 16:4. [PMID: 38438932 PMCID: PMC10913398 DOI: 10.1186/s41479-024-00125-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 01/09/2024] [Indexed: 03/06/2024] Open
Abstract
AIM This study aimed to examine the utility of simultaneously performed the Film Array pneumonia panels (pneumonia panels) and Gram staining with the same specimens and evaluate their effect on antimicrobial selection. METHODS This prospective study, conducted from April 2022 to January 2023, enrolled adult patients with pneumonia, including those with ventilator-associated pneumonia (VAP). Specimens obtained at the time of sputum culture were tested using Gram staining and the pneumonia panel. The patients' characteristics and pneumonia panel results were assessed. We also evaluated the selection of antimicrobial agents for drug-resistant bacteria detected by the pneumonia panel. RESULTS This study comprised 39 patients: 25 patients (64.1%) underwent intubation, including 7 (17.9%) patients with VAP. Most tests were performed at the time of admission, while some were performed during hospitalization. Good quality sputum was obtained from intubated patients. The pneumonia panel detected drug-resistant bacteria in 12 cases. Six patients required antimicrobial escalation, while the antimicrobial regimen remained unchanged for 2 patients in whom Pseudomonas aeruginosa was detected and had already received meropenem. The attending physician did not change the antimicrobials, considering the results of Gram staining and the patient's general condition in 4 patients. CONCLUSIONS The pneumonia panel might be useful for detecting drug-resistant organisms at an early stage. It may be important to take the Gram staining results and the patient's condition into account with pneumonia panel for appropriate antibiotic prescription.
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Affiliation(s)
- Hiroshi Matsuura
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan.
| | - Koudai Arimoto
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan
| | - Yoshihito Takahashi
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan
| | - Masafumi Kishimoto
- Osaka Prefectural Nakakawachi Emergency and Critical Care Center, 3-4-13 Nishiiwata, Higashiosaka, Osaka, 578-0947, Japan
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12
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Ben Lahlou Y, Eddair Y, Dokponou YCH, Elouennass M, Chadli M. The Evaluation of the BioFire FilmArray Meningitis/Encephalitis Panel for the Detection of Bacteria and Yeast in Cerebrospinal Fluid Specimens. Cureus 2024; 16:e56260. [PMID: 38623118 PMCID: PMC11017369 DOI: 10.7759/cureus.56260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 04/17/2024] Open
Abstract
Background and objective Infectious meningitis and encephalitis are serious diseases that can have fatal consequences, especially in the case of bacterial meningitis. Molecular biology has made it possible to quickly introduce appropriate treatment. Our study aims to evaluate the FilmArray Meningitis/Encephalitis Polymerase Chain Reaction (PCR) Panel (BioFire Diagnostics, Salt Lake City, Utah) implemented in our department compared to traditional methods. Material and methods This was a retrospective single-center study conducted in the Department of Bacteriology of Mohammed V Military Training Hospital, Rabat, for a period of four years. All cerebrospinal fluid (CSF) samples from patients with symptoms of meningitis or meningoencephalitis submitted to the laboratory for cytobacteriological analysis were included in the study. Conventional analysis has been compared with molecular biology. Results The overall agreement rate with FilmArray in our study was 86%. The sensitivity to Escherichia coli K1, Haemophilus influenzae, Neisseria meningitidis, Streptococcus agalactiae, and Streptococcus pneumoniae was 100%. And for Cryptococcus neoformans it was 83% in our study. Conclusion In summary, this technique can be used to diagnose bacterial meningitis more sensitively than with conventional techniques, while at the same time allowing a rapid and efficacious patient's treatment.
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Affiliation(s)
- Yassine Ben Lahlou
- Bacteriology, Mohammed V Military Training Hospital, Mohammed V University, Rabat, MAR
| | - Yassine Eddair
- Bacteriology, Mohammed V Military Training Hospital, Mohammed V University, Rabat, MAR
| | | | - Mostapha Elouennass
- Bacteriology, Mohammed V Military Training Hospital, Mohammed V University, Rabat, MAR
| | - Mariama Chadli
- Bacteriology, Mohammed V Military Training Hospital, Mohammed V University, Rabat, MAR
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13
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Pickens CI, Wunderink RG. Novel and Rapid Diagnostics for Common Infections in the Critically Ill Patient. Infect Dis Clin North Am 2024; 38:51-63. [PMID: 38280767 DOI: 10.1016/j.idc.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
There are several novel platforms that enhance detection of pathogens that cause common infections in the intensive care unit. These platforms have a sample to answer time of a few hours, are often higher yield than culture, and have the potential to improve antibiotic stewardship.
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Affiliation(s)
- Chiagozie I Pickens
- Department of Medicine, Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, 303 E. Superior Street Simpson Querrey 5th Floor, Suite 5-406, Chicago, IL 60611-2909, USA.
| | - Richard G Wunderink
- Department of Medicine, Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, 303 E. Superior Street Simpson Querrey 5th Floor, Suite 5-406, Chicago, IL 60611-2909, USA
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14
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Boers SA, van Houdt R, van Sorge NM, Groot J, van Aarle Y, van Bussel MJAWM, Smit LFE, Wessels E, Claas ECJ. A multicenter evaluation of the QIAstat-Dx meningitis-encephalitis syndromic test kit as compared to the conventional diagnostic microbiology workflow. Eur J Clin Microbiol Infect Dis 2024; 43:511-516. [PMID: 38206519 PMCID: PMC10917839 DOI: 10.1007/s10096-024-04751-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
PURPOSE Rapid diagnosis and treatment of infectious meningitis and encephalitis (ME) is critical to minimize morbidity and mortality. Recently, Qiagen introduced the CE-IVD QIAstat-Dx ME panel (QS-ME) for syndromic diagnostic testing of meningitis and encephalitis. Some data on the performance of the QS-ME in comparison to the BioFire FilmArray ME panel are available. In this study, the performance of the QS-ME is compared to the current diagnostic workflow in two academic medical centers in the Netherlands. METHODS A total of 110 cerebrospinal fluid samples were retrospectively tested with the QS-ME. The results obtained were compared to the results of laboratory-developed real-time PCR assays (LDTs), IS-pro, bacterial culture, and cryptococcal antigen (CrAg) testing. In addition, the accuracy of the QS-ME was also investigated using an external quality assessment (EQA) panel consisting of ten samples. RESULTS Four of the 110 samples tested failed to produce a valid QS-ME result. In the remaining 106 samples, the QS-ME detected 53/53 viral targets, 38/40 bacterial targets, and 7/13 Cryptococcus neoformans targets. The discrepant bacterial results consisted of two samples that were previously tested positive for Listeria monocytogenes (CT 35.8) and Streptococcus pneumoniae (CT 40), respectively. The QS-ME detected one additional result, consisting of a varicella-zoster virus signal (CT 35.9), in a sample in which both techniques detected Streptococcus pyogenes. Finally, 100% concordance was achieved in testing a blinded bacterial ME EQA panel. CONCLUSION The QS-ME is a relevant addition to the syndromic testing landscape to assist in diagnosing infectious ME.
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Affiliation(s)
- Stefan A Boers
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
| | - Robin van Houdt
- Dept. Medical Microbiology and Infection prevention, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Nina M van Sorge
- Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam UMC location AMC, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Jelle Groot
- Dept. Medical Microbiology and Infection prevention, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Yvette van Aarle
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Mario J A W M van Bussel
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Louise F E Smit
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Els Wessels
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Eric C J Claas
- Dept. Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
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15
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Milburn J, Suresh R, Doyle R, Jarvis JN. The diagnosis of central nervous system infections in resource-limited settings and the use of novel and molecular diagnostic platforms to improve diagnosis. Expert Rev Mol Diagn 2024; 24:219-230. [PMID: 38369939 DOI: 10.1080/14737159.2024.2317414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
INTRODUCTION Central nervous system infections (CNSI) disproportionately affect individuals in low-resource settings where diagnosis is challenging; large proportions of patients never receive a confirmed microbiological diagnosis resulting in inadequate management and high mortality. The epidemiology of CNSI varies globally and conventional diagnostics deployed in resource-limited settings have significant limitations, with an urgent need for improved diagnostic strategies. AREAS COVERED This review describes molecular platforms and other novel diagnostics used in the diagnosis of CNSI that are applicable to resource-limited settings. An extensive literature search of Medline and PubMed was performed. The emphasis is on investigations targeting infections of relevance to resource-limited settings either due to variation in regional CNSI epidemiology or due to increased prevalence in patients with immunosuppression. This includes commercially available multiplex PCR platforms, mycobacterial PCR platforms, and rapid diagnostics tests. To offer a framework for the optimal implementation in clinical settings, existing evidence highlighting the advantages and limitations of available platforms is reviewed. EXPERT OPINION The implementation of molecular platforms and other novel diagnostics has the potential to transform CNSI diagnosis in resource-limited settings, with several examples of successful rollout of novel diagnostics such as Xpert MTB/RIF Ultra and cryptococcal antigen testing.
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Affiliation(s)
- James Milburn
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Clinical Research, Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Rachita Suresh
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Ronan Doyle
- Department of Clinical Research, Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Joseph N Jarvis
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Clinical Research, Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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16
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Ivaska L, Herberg J, Sadarangani M. Distinguishing community-acquired bacterial and viral meningitis: Microbes and biomarkers. J Infect 2024; 88:106111. [PMID: 38307149 DOI: 10.1016/j.jinf.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
Diagnostic tools to differentiate between community-acquired bacterial and viral meningitis are essential to target the potentially lifesaving antibiotic treatment to those at greatest risk and concurrently spare patients with viral meningitis from the disadvantages of antibiotics. In addition, excluding bacterial meningitis and thus decreasing antibiotic consumption would be important to help reduce antimicrobial resistance and healthcare expenses. The available diagnostic laboratory tests for differentiating bacterial and viral meningitis can be divided microbiological pathogen-focussed methods and biomarkers of the host response. Bacterial culture-independent microbiological methods, such as highly multiplexed nucleic acid amplification tests, are rapidly making their way into the clinical practice. At the same time, more conventional host protein biomarkers, such as procalcitonin and C-reactive protein, are supplemented by newer proteomic and transcriptomic signatures. This review aims to summarise the current state and the recent advances in diagnostic methods to differentiate bacterial from viral meningitis.
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Affiliation(s)
- Lauri Ivaska
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Savitehtaankatu 5, 20521 Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Kiinanmyllynkatu 10, 20520 Turku, Finland.
| | - Jethro Herberg
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, Norfolk Place, London, United Kingdom.
| | - Manish Sadarangani
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada.
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17
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Sunnerhagen T, Widén J, Handhal S, Özkaya Şahin G. A retrospective observational study of 1000 consecutive patients tested with the FilmArray® Meningitis/Encephalitis panel: clinical diagnosis at discharge and microbiological findings. Sci Rep 2024; 14:4015. [PMID: 38369552 PMCID: PMC10874959 DOI: 10.1038/s41598-024-54621-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/14/2024] [Indexed: 02/20/2024] Open
Abstract
FilmArray® Meningitis/Encephalitis panel (FAME-p) is used to diagnose central nervous system (CNS) infections. In this study, we investigated performance of FAME-p compared to comparator assays (CA), and for the first time, clinical diagnosis at discharge (CDD). 1000 consecutive patients with a cerebrospinal fluid (CSF) sample analyzed with FAME-p were identified. As CA, culture, polymerase chain reaction and cryptococcal antigen test were used. Medical records of patients were obtained. A CDD of CNS infection was made in 139 of 1000 CSF samples. FAME-p was positive in 66 samples with 44 viral and 22 bacterial agents. Thirteen FAME-p findings were not confirmed by CA, with four discrepant results remaining after comparison with the CDD. Positive percentage agreement (PPA) calculated against CA was 100%. Negative percentage agreement (NPA) calculated against CA was 94.4-99.8% for Haemophilus influenzae, Listeria monocytogenes, Streptococcus agalactiae, S. pneumoniae and varicella-zoster virus (VZV). NPA calculated against CDD was higher (compared to CA) for L. monocytogenes, S. agalactiae and VZV (100%), and lower for Escherichia coli, enterovirus and herpes simplex virus 2 (50-83.3%). NPA of FAME-p for human herpes virus 6 was difficult to interpret. Eighty-four cases received diagnosis of CNS-infection despite negative FAME-p. The four most common non-infectious etiologies were primary headache disorders, cranial nerve palsies, neuroinflammatory disorders and seizure. Although FAME-p shows good performance in diagnosis of CNS infections, result of FAME-p should be interpreted carefully. Considering infectious diseases not covered by FAME-p as well as non-infectious differential diagnoses is important in this context.
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Affiliation(s)
- Torgny Sunnerhagen
- Clinical Microbiology, Infection Prevention and Control, Office for Medical Services, Region Skåne, Lund, Sweden.
- Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
| | - Johan Widén
- Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Clinic of Infectious Diseases, Skåne University Hospital, Lund, Sweden
| | - Sahar Handhal
- Clinical Microbiology, Infection Prevention and Control, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Gülşen Özkaya Şahin
- Clinical Microbiology, Infection Prevention and Control, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Medical Microbiology, Department of Laboratory Medicine Lund, Medical Faculty, Lund University, Lund, Sweden
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18
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López N, Cuesta G, Rodríguez-Vega S, Rosas E, Chumbita M, Casals-Pascual C, Morata L, Vergara A, Bodro M, Bosch J, Herrera S, Martínez JA, Mensa J, Garcia-Vidal C, Marcos MÁ, Vila J, Soriano A, Puerta-Alcalde P. Multiplex real-time PCR FilmArray performance in the diagnosis of meningoencephalitis: lights and shadows. Infection 2024; 52:165-172. [PMID: 37515691 PMCID: PMC10810907 DOI: 10.1007/s15010-023-02076-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/13/2023] [Indexed: 07/31/2023]
Abstract
PURPOSE We aimed to evaluate the performance of the FilmArray (FA) meningitis/encephalitis (ME) panel. Secondarily, we analyzed the false positive (FP) and false negative (FN) results, as well as the predictive values of the technique, regarding the cerebrospinal fluid (CSF) characteristics. METHODS FA is a multiplex real-time PCR detecting 14 of the most common ME pathogens in CSF. All FA performed at our hospital (2018-2022) were retrospectively reviewed. FA was compared to conventional techniques and its performance was assessed based on the final diagnosis of the episode. RESULTS FA was performed in 313 patients with suspicion of ME. Most patients had altered mental status (65.2%) and fever (61%). Regarding CSF characteristics, 49.8% and 53.7% presented high CSF proteins and pleocytosis, respectively. There were 84 (26.8%) positive FA results, mainly for HSV-1 (10.9%), VZV (5.1%), Enterovirus (2.6%), and S. pneumoniae (1.9%). In the 136 cases where both FA and routine methods were performed, there was a 25.7% lack of agreement. We identified 6.6% FN results, but 28.6% FP, mainly due to HSV-1. This resulted in a high negative predictive value (NPV) of 93.4%, but a positive predictive value (PPV) of 73%. Remarkably, PPV as low as 36.9%, and 70.2%, were found in cases without pleocytosis, or lack of high CSF protein levels, respectively. CONCLUSION FA was associated with high NPV, but frequent FP results and low PPV, particularly for HSV-1, and especially in patients without high CSF protein levels or pleocytosis.
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Affiliation(s)
- Néstor López
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Genoveva Cuesta
- Microbiology Department, Hospital Clinic, University of Barcelona, ISGLOBAL, Barcelona, Spain
| | | | - Enric Rosas
- Microbiology Department, Hospital Clinic, University of Barcelona, ISGLOBAL, Barcelona, Spain
| | - Mariana Chumbita
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Climent Casals-Pascual
- Microbiology Department, Hospital Clinic, University of Barcelona, ISGLOBAL, Barcelona, Spain
- CIBERINF, CIBER Infectious Diseases, Madrid, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Laura Morata
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Andrea Vergara
- Microbiology Department, Hospital Clinic, University of Barcelona, ISGLOBAL, Barcelona, Spain
| | - Marta Bodro
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Jordi Bosch
- Microbiology Department, Hospital Clinic, University of Barcelona, ISGLOBAL, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Sabina Herrera
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Jose Antonio Martínez
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Barcelona, Spain
- CIBERINF, CIBER Infectious Diseases, Madrid, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Josep Mensa
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Barcelona, Spain
| | - Carolina Garcia-Vidal
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Barcelona, Spain
- CIBERINF, CIBER Infectious Diseases, Madrid, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - María Ángeles Marcos
- Microbiology Department, Hospital Clinic, University of Barcelona, ISGLOBAL, Barcelona, Spain
- CIBERINF, CIBER Infectious Diseases, Madrid, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Jordi Vila
- Microbiology Department, Hospital Clinic, University of Barcelona, ISGLOBAL, Barcelona, Spain
- CIBERINF, CIBER Infectious Diseases, Madrid, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Alex Soriano
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Barcelona, Spain
- CIBERINF, CIBER Infectious Diseases, Madrid, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Pedro Puerta-Alcalde
- Infectious Diseases Department, Hospital Clínic-IDIBAPS, Barcelona, Spain.
- Universitat de Barcelona (UB), Barcelona, Spain.
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19
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Niemelä S, Lempinen L, Löyttyniemi E, Grönroos JO, Luoto R, Peltola V, Jero J. Finnish paediatric study found a low incidence of bacterial meningitis from 2011 to 2018 but a substantial proportion of nosocomial meningitis. Acta Paediatr 2024; 113:327-335. [PMID: 37800382 DOI: 10.1111/apa.16991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023]
Abstract
AIM This study examined the predisposing factors, clinical picture, bacterial aetiology and clinical outcomes of infants and children with bacterial meningitis (BM). METHODS The medical records of patients under 16 years of age, treated by Turku University Hospital, Finland, from 2011 to 2018, were screened for meningitis using the International Classification of Diseases, Tenth Revision codes. Patients were included if bacteria were detected in cerebrospinal fluid (CSF) or other predefined laboratory variables indicated BM, despite CSF testing negative for bacteria. The Glasgow Outcome Scale (GOS) was used to determine outcomes. RESULTS We identified 37 children with BM: 22 infants aged 0-89 days and 15 children aged 90 days to 15 years. The overall incidence was approximately 5.7/100 000/year. Nosocomial meningitis was documented in 51%. Bacterial growth was detected in the CSF or blood cultures of the majority of patients (57%). Escherichia coli (14%), group B streptococcus (11%) and Streptococcus pneumoniae (8%) were the most common pathogens. There were 14% of patients with unfavourable outcomes, namely GOS scores of 1-4, but no deaths. CONCLUSION The incidence of paediatric BM was low during the study period, but the proportion of nosocomial meningitis was substantial. The frequency of unfavourable long-term outcomes was relatively low.
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Affiliation(s)
- Sakke Niemelä
- Department of Otorhinolaryngology, Turku University Hospital, University of Turku, Turku, Finland
| | - Laura Lempinen
- Department of Radiology, HUS Medical Imaging Center, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Eliisa Löyttyniemi
- Department of Biostatistics, Turku University Hospital, University of Turku, Turku, Finland
| | - Juha O Grönroos
- Department of Clinical Microbiology, Turku University Hospital, University of Turku, Turku, Finland
| | - Raakel Luoto
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, University of Turku, Turku, Finland
| | - Ville Peltola
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, University of Turku, Turku, Finland
| | - Jussi Jero
- Department of Otorhinolaryngology, Head and Neck Surgery, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
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20
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Chong PF, Higashi K, Matsuoka W, Arimura K, Sangatsuda Y, Iwaki K, Sonoda Y, Ichimiya Y, Kamori A, Kawakami A, Mizuguchi S, Kaku N, Sakai Y, Ohga S. Persistent intracranial hyper-inflammation in ruptured cerebral aneurysm after COVID-19: case report and review of the literature. BMC Neurol 2024; 24:17. [PMID: 38166683 PMCID: PMC10759412 DOI: 10.1186/s12883-023-03493-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The systemic manifestations of coronavirus disease 2019 (COVID-19) include hyperinflammatory reactions in various organs. Recent studies showed evidence for the frequent involvement of central nervous system in affected patients; however, little is known about clinical features of cerebrovascular diseases in childhood-onset COVID-19. CASE PRESENTATION A 10-year-old boy recovered from SARS-CoV-2 infection without complication. On 14 days after infection, he presented with loss of consciousness. A head computed tomography detected a ruptured cerebral aneurysm at the left posterior cerebral artery accompanying subarachnoid hemorrhage (SAH). Immediate surgical intervention did not rescue the patient, resulting in the demise 7 days after admission. Serological and genetic tests excluded the diagnosis of vasculitis and connective tissue disorders. Retrospective analysis showed markedly higher levels of interleukin (IL)-1β, IL-6 and IL-8 in the cerebrospinal fluid than the serum sample concurrently obtained. A review of literature indicated that adult patients with COVID-19 have a risk for the later development of SAH during the convalescent phase of COVID-19. CONCLUSIONS SAH is a severe complication of COVID-19 in children and adults who have asymptomatic cerebrovascular aneurysms. The markedly high levels of cytokines detected in the cerebrospinal fluid suggested that intracranial hyperinflammatory condition might be one of the possible mechanisms involved in the rupture of a preexisting cerebrovascular aneurysms.
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Affiliation(s)
- Pin Fee Chong
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Kanako Higashi
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
- Emergency and Critical Care Center, Kyushu University Hospital, Fukuoka, 812-8582, Japan
| | - Wakato Matsuoka
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
- Emergency and Critical Care Center, Kyushu University Hospital, Fukuoka, 812-8582, Japan
| | - Koichi Arimura
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Katsuma Iwaki
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yuri Sonoda
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
- Research Center for Environment and Developmental Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yuko Ichimiya
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Akiko Kamori
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Akiko Kawakami
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
- Emergency and Critical Care Center, Kyushu University Hospital, Fukuoka, 812-8582, Japan
| | - Soichi Mizuguchi
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
- Emergency and Critical Care Center, Kyushu University Hospital, Fukuoka, 812-8582, Japan
| | - Noriyuki Kaku
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
- Emergency and Critical Care Center, Kyushu University Hospital, Fukuoka, 812-8582, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan.
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
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21
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Ghoweba Y, Safizadeh Shabestari SA, Malik ZA. Diagnostic Accuracy of Cerebrospinal Fluid Multiplex Polymerase Chain Reaction Panel Testing in Patients With Suspected Central Nervous System Infections: A Multi-Center Study in the United Arab Emirates. Cureus 2024; 16:e51906. [PMID: 38333447 PMCID: PMC10851033 DOI: 10.7759/cureus.51906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 12/28/2023] [Indexed: 02/10/2024] Open
Abstract
Background Delays in diagnosis and treatment of central nervous system (CNS) infections can lead to significant morbidity and mortality among children and adults. Prior antibiotic treatment is a major hurdle to accurate diagnosis due to falsely negative cerebrospinal fluid (CSF) cultures in partially treated patients. Increasingly, molecular diagnostic methods using multiplex polymerase chain reaction (mPCR) testing on CSF samples are being utilized in clinical practice for timely and accurate diagnosis. However, there is no data regarding the diagnostic accuracy or clinical impact of CSF mPCR testing in the Middle East region. We sought to compare the diagnostic accuracy of an automated mPCR CSF panel with routine CSF culture, the current gold standard, in the United Arab Emirates (UAE). Methods This single-gated, multi-center, diagnostic accuracy study included patients from birth onwards who were admitted to any of the three participating hospitals with an initial diagnosis of meningitis or encephalitis, between January 2017 and March 2021, and had CSF samples collected for mPCR and culture. Sociodemographic, clinical, and molecular data were collected for all. Results A total of 353 CSF samples were collected from patients from 0-90 years old hospitalized for suspected CNS infection. Children constituted 51% of the study population, and males were slightly over-represented (55.2%). Pathogens were detected by mPCR in 78 (22%) CSF samples, of which 19 (24%) were bacteria and 59 (76%) were viruses. No fungal pathogens were detected. Enteroviruses were the most prevalent CNS pathogen among our cohort (40%), followed by herpes simplex virus type 2 (HSV-2) (12.5%). Children constituted 69% of positive samples for enterovirus, while HSV-2 was exclusively detected among adults. Using CSF culture as the diagnostic gold standard, the mPCR panel demonstrated high specificity (100%) and sensitivity (96.3%) in diagnosing CNS infection among all age groups. mPCR testing demonstrated a high overall percentage of agreement (OPA) with CSF culture (98.9%). Patients with bacterial meningitis had a significantly longer hospitalization (p=0.004) and duration of antibiotic therapy (p=0.001) compared to those with viral meningitis. Three CSF samples were negative on mPCR testing but positive on culture. These pathogens included: methicillin-sensitive Staphylococcus aureus(MSSA), Bacillus cereus, and Mycobacterium Tuberculosis (MTB). In addition, 13 patients had negative CSF cultures but tested positive on CSF mPCR. These pathogens included Streptococcus pneumoniae (seven patients), Haemophilus influenzae (three patients), Streptococcus agalactiae (two patients), and Escherichia coli (one patient). All discordant results were confirmed by reviewing the patient's clinical presentation, CSF analysis, clinical course, and final diagnosis. Conclusion CSF mPCR panel is a highly sensitive and specific diagnostic tool for the diagnosis of CNS infections among all age groups in the UAE. Routine use of CSF mPCR panels can decrease healthcare costs by reducing the length of stay and can also aid antibiotic stewardship efforts by reducing antibiotic overuse in patients with viral CSF infections. CSF culture and mPCR complement each other by identifying CNS pathogens in patients with prior antibiotic exposure who would otherwise be missed if relying on CSF culture alone. However, concomitant CSF culture samples should be sent to avoid missing unusual CNS pathogens.
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Affiliation(s)
- Yousra Ghoweba
- Pediatrics, Mohammed Bin Rashid University Of Medicine and Health Sciences, Dubai, ARE
| | | | - Zainab A Malik
- Pediatrics and Pediatric Infectious Diseases, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, ARE
- Pediatrics and Pediatric Infectious Diseases, Genesis Healthcare, Dubai, ARE
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22
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Liu BM, Mulkey SB, Campos JM, DeBiasi RL. Laboratory diagnosis of CNS infections in children due to emerging and re-emerging neurotropic viruses. Pediatr Res 2024; 95:543-550. [PMID: 38042947 DOI: 10.1038/s41390-023-02930-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/10/2023] [Accepted: 11/05/2023] [Indexed: 12/04/2023]
Abstract
Recent decades have witnessed the emergence and re-emergence of numerous medically important viruses that cause central nervous system (CNS) infections in children, e.g., Zika, West Nile, and enterovirus/parechovirus. Children with immature immune defenses and blood-brain barrier are more vulnerable to viral CNS infections and meningitis than adults. Viral invasion into the CNS causes meningitis, encephalitis, brain imaging abnormalities, and long-term neurodevelopmental sequelae. Rapid and accurate detection of neurotropic viral infections is essential for diagnosing CNS diseases and setting up an appropriate patient management plan. The addition of new molecular assays and next-generation sequencing has broadened diagnostic capabilities for identifying infectious meningitis/encephalitis. However, the expansion of test menu has led to new challenges in selecting appropriate tests and making accurate interpretation of test results. There are unmet gaps in development of rapid, sensitive and specific molecular assays for a growing list of emerging and re-emerging neurotropic viruses. Herein we will discuss the advances and challenges in the laboratory diagnosis of viral CNS infections in children. This review not only sheds light on selection and interpretation of a suitable diagnostic test for emerging/re-emerging neurotropic viruses, but also calls for more research on development and clinical utility study of novel molecular assays. IMPACT: Children with immature immune defenses and blood-brain barrier, especially neonates and infants, are more vulnerable to viral central nervous system infections and meningitis than adults. The addition of new molecular assays and next-generation sequencing has broadened diagnostic capabilities for identifying infectious meningitis and encephalitis. There are unmet gaps in the development of rapid, sensitive and specific molecular assays for a growing list of emerging and re-emerging neurotropic viruses.
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Affiliation(s)
- Benjamin M Liu
- Division of Pathology and Laboratory Medicine, Children's National Hospital, Washington, DC, USA.
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
- Department of Pathology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
- Children's National Research Institute, Washington, DC, USA.
- The District of Columbia Center for AIDS Research, Washington, DC, USA.
| | - Sarah B Mulkey
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Children's National Research Institute, Washington, DC, USA
- Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
- Division of Neurology, Children's National Hospital, Washington, DC, USA
- Department of Neurology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Joseph M Campos
- Division of Pathology and Laboratory Medicine, Children's National Hospital, Washington, DC, USA
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Department of Pathology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Roberta L DeBiasi
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
- Children's National Research Institute, Washington, DC, USA.
- Division of Pediatric Infectious Diseases, Children's National Hospital, Washington, DC, USA.
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23
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Lawrence SM, Goshia T, Sinha M, Fraley SI, Williams M. Decoding human cytomegalovirus for the development of innovative diagnostics to detect congenital infection. Pediatr Res 2024; 95:532-542. [PMID: 38146009 PMCID: PMC10837078 DOI: 10.1038/s41390-023-02957-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023]
Abstract
Cytomegalovirus is the most common cause of congenital infectious disease and the leading nongenetic etiology of sensorineural hearing loss. Although most infected neonates are asymptomatic at birth, congenital cytomegalovirus infection is responsible for nearly 400 infant deaths annually in the United States and may lead to significant long-term neurodevelopmental impairments in survivors. The resulting financial and social burdens of congenital cytomegalovirus infection have led many medical centers to initiate targeted testing after birth, with a growing advocacy to advance universal newborn screening. While no cures or vaccines are currently available to eliminate or prevent cytomegalovirus infection, much has been learned over the last five years regarding disease pathophysiology and viral replication cycles that may enable the development of innovative diagnostics and therapeutics. This Review will detail our current understanding of congenital cytomegalovirus infection, while focusing our discussion on routine and emerging diagnostics for viral detection, quantification, and long-term prognostication. IMPACT: This review highlights our current understanding of the fetal transmission of human cytomegalovirus. It details clinical signs and physical findings of congenital cytomegalovirus infection. This submission discusses currently available cytomegalovirus diagnostics and introduces emerging platforms that promise improved sensitivity, specificity, limit of detection, viral quantification, detection of genomic antiviral resistance, and infection staging (primary, latency, reactivation, reinfection).
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Affiliation(s)
- Shelley M Lawrence
- University of Utah, College of Medicine, Department of Pediatrics, Division of Neonatology, Salt Lake City, UT, USA.
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | | | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
| | - Marvin Williams
- University of Oklahoma, College of Medicine, Department of Obstetrics and Gynecology, Division of Fetal-Maternal Medicine, Oklahoma City, OK, USA
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24
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Côrtes LGF, Maldonado MM, Koga PCM, Santiago KADS, Fernandes GBP, Maluf MM, Martino MDV. Evaluation of pathogen from the FilmArray meningitis/encephalitis panel and recommendations on atypical findings. ARQUIVOS DE NEURO-PSIQUIATRIA 2024; 82:1-8. [PMID: 38316425 PMCID: PMC10843913 DOI: 10.1055/s-0044-1779035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 10/04/2023] [Indexed: 02/07/2024]
Abstract
BACKGROUND Infectious meningoencephalitis is a potentially fatal clinical condition that causes inflammation of the central nervous system secondary to the installation of different microorganisms. The FilmArray meningitis/encephalitis panel allows the simultaneous detection of 14 pathogens with results in about one hour. OBJECTIVE This study is based on retrospectively evaluating the implementation of the FilmArray meningitis/encephalitis panel in a hospital environment, highlighting the general results and, especially, analyzing the consistency of the test results against the clinical and laboratory conditions of the patients. METHODS Data were collected through the results reported by the BioFire FilmArray system software from the meningitis/encephalitis panel. The correlated laboratory tests used in our analysis, when available, included biochemical, cytological, direct and indirect microbiological tests. RESULTS In the analyzed period, there were 496 samples with released results. Of the total of 496 samples analyzed, 88 (17.75%) were considered positive, and 90 pathogens were detected, and in 2 of these (2.27%) there was co-detection of pathogens. Viruses were the agents most frequently found within the total number of pathogens detected. Of the 496 proven samples, 20 (4.03%) were repeated, 5 of which were repeated due to invalid results, 6 due to the detection of multiple pathogens and 9 due to disagreement between the panel results and the other laboratory tests and/or divergence of the clinical-epidemiological picture. Of these 20 repeated samples, only 4 of them (20%) maintained the original result after repeating the test, with 16 (80%) being non-reproducible. The main factor related to the disagreement of these 16 samples during retesting was the detection of bacterial agents without any relationship with other laboratory tests or with the patients' clinical condition. CONCLUSION In our study, simply reproducing tests with atypical results from the FilmArray meningitis/encephalitis panel proved, in most cases, effective and sufficient for interpreting these results.
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25
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Kitagawa D, Kitano T, Uchihara Y, Ando T, Nishikawa H, Suzuki R, Onaka M, Kasamatsu T, Shiraishi N, Takemoto K, Sekine M, Suzuki S, Suzuki Y, Nakano A, Nakano R, Yano H, Yoshida S, Kawahara M, Maeda K, Nakamura F. Impact of Multiplex Polymerase Chain Reaction Test in Patients With Meningitis or Encephalitis. Open Forum Infect Dis 2023; 10:ofad634. [PMID: 38156045 PMCID: PMC10753909 DOI: 10.1093/ofid/ofad634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/15/2023] [Indexed: 12/30/2023] Open
Abstract
Background The objective of this study was to evaluate the impact of the FilmArray meningitis/encephalitis panel (FAME) on length of stay (LOS) and duration of antimicrobial treatment in children and adults in a Japanese community hospital. Methods This retrospective cohort study was conducted in Japan between January 2016 and December 2022. We included hospitalized patients with cerebrospinal fluid (CSF) samples and those aged <2 months or who had 5 or more white blood cells/μL in the CSF. To compare the days of therapy (DOT) and LOS between the pre-FAME and FAME periods, multivariate Poisson regression analyses were conducted without an offset term. Results The number of cases undergoing pathogen-specific polymerase chain reaction increased from 3.7% in the pre-FAME period to 57.5% in the FAME period (P < .001). The pathogen identification rate also increased during the FAME period, from 0.4% to 18.7% (P < .001). While the antibacterial DOT was not statistically different between the 2 periods (adjusted rate ratio [aRR], 1.06 [95% confidence interval {CI}, 1.00-1.13]; P = .063]), the antiviral DOT was significantly shorter in the FAME period (aRR, 0.80 [95% CI, .71-.89]; P < .001). Conclusions This study revealed a significant reduction in antiviral use during the FAME period, whereas LOS and antibacterial use did not decrease. Given the possibility of factors (eg, the COVID-19 pandemic) affecting the epidemiology of meningitis and encephalitis, the indications and impact of the FAME test should be evaluated with continuous monitoring of the epidemiology of meningitis and encephalitis and its clinical impact.
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Affiliation(s)
- Daisuke Kitagawa
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Taito Kitano
- Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Yuto Uchihara
- Department of Neurology, Nara Prefecture General Medical Center, Nara, Japan
| | - Takafusa Ando
- Department of Neurology, Nara Prefecture General Medical Center, Nara, Japan
| | - Hiroki Nishikawa
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Rika Suzuki
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Masayuki Onaka
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Takehito Kasamatsu
- Department of Infectious Diseases, Nara Prefecture General Medical Center, Nara, Japan
| | - Naoyuki Shiraishi
- Department of Infectious Diseases, Nara Prefecture General Medical Center, Nara, Japan
| | - Kiyoshi Takemoto
- Department of Critical Care Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Madoka Sekine
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Soma Suzuki
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
| | - Yuki Suzuki
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Ryuichi Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Hisakazu Yano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Japan
| | - Sayaka Yoshida
- Department of Pediatrics, Nara Prefecture General Medical Center, Nara, Japan
| | - Makoto Kawahara
- Department of Neurology, Nara Prefecture General Medical Center, Nara, Japan
| | - Koichi Maeda
- Department of Infectious Diseases, Nara Prefecture General Medical Center, Nara, Japan
| | - Fumihiko Nakamura
- Department of Laboratory Medicine, Nara Prefecture General Medical Center, Nara, Japan
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26
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Lewinski MA, Alby K, Babady NE, Butler-Wu SM, Bard JD, Greninger AL, Hanson K, Naccache SN, Newton D, Temple-Smolkin RL, Nolte F. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 2023; 25:857-875. [PMID: 37757952 DOI: 10.1016/j.jmoldx.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.
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Affiliation(s)
- Michael A Lewinski
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Roche Molecular Systems, San Clemente, California.
| | - Kevin Alby
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - N Esther Babady
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan M Butler-Wu
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Dien Bard
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander L Greninger
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Kimberly Hanson
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah
| | - Samia N Naccache
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Microbiology, LabCorp Seattle, Seattle, Washington
| | - Duane Newton
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Bio-Rad Laboratories, Irvine, California
| | | | - Frederick Nolte
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
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27
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García-Sánchez C, Bloise I, García-Rodríguez J, Cendejas-Bueno E. Are cerebrospinal fluid biochemical parameters valid to predict positive results in microbiological molecular diagnostic platforms? A 4-year experience with the FilmArray® Panel Meningitis/Encephalitis for detection of community-acquired bacterial meningitis. Diagn Microbiol Infect Dis 2023; 107:116031. [PMID: 37595339 DOI: 10.1016/j.diagmicrobio.2023.116031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 07/10/2023] [Accepted: 07/15/2023] [Indexed: 08/20/2023]
Abstract
OBJECTIVE To demonstrate whether the use of the FilmArray® Meningitis/Encephalitis panel (M/E) in the diagnosis of bacterial meningitis can be optimized based on the screening of cerebrospinal fluid biochemical parameters and whether there is a correlation between biochemical data and positive results of the technique. MATERIAL AND METHODS We used data from La Paz University Hospital between September 5, 2017 and December 1, 2021, from patients who had had the FilmArray® panel M/E performed on cerebrospinal fluid samples. RESULTS Bacterial meningitis was suspected in 63.9% of the patients; 38.15% had a positive result on the FilmArray® panel M/E, of which 68.97% were isolated in culture. Of the biochemical parameters studied in cerebrospinal fluid, white blood cell count, lactate, and protein were increased in PCR-positive patients, but glucose was decreased. DISCUSSION Only lactate showed a significant contribution to the model, with a cut-off point of 4.65 mmol/L with a sensitivity of 81.5% and a specificity of 96.4%.
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Affiliation(s)
| | - Iván Bloise
- Clinical Microbiology Department, Hospital Universitario La Paz, IdiPaz, Madrid, Spain
| | | | - Emilio Cendejas-Bueno
- Clinical Microbiology Department, Hospital Universitario La Paz, IdiPaz, Madrid, Spain; CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
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28
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Sundelin T, Bialas J, de Diego J, Hermanowski M, Leibhan H, Ponderand L, Juanola-Falgarona M, Jones T, Rey M, Johnson S, Pareja J, Caspar Y. Evaluation of the QIAstat-Dx Meningitis/Encephalitis Panel, a multiplex PCR platform for the detection of community-acquired meningoencephalitis. J Clin Microbiol 2023; 61:e0042623. [PMID: 37702495 PMCID: PMC10595057 DOI: 10.1128/jcm.00426-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/17/2023] [Indexed: 09/14/2023] Open
Abstract
Rapid identification of the causative pathogens of central nervous system infections is essential for providing appropriate management and improving patient outcomes. The performance of QIAstat-Dx Meningitis/Encephalitis (ME) Panel-a multiplex PCR testing platform-in detecting pathogens implicated in meningitis and/or encephalitis was evaluated using BioFire FilmArray ME Panel as a comparator method. This multicenter study analyzed 585 retrospective residual cerebrospinal fluid specimens and 367 contrived specimens. The QIAstat-Dx ME Panel showed positive percent agreement (PPA) values of 100% for Neisseria meningitidis, Streptococcus agalactiae, Escherichia coli K1, Listeria monocytogenes, and Cryptococcus gattii/neoformans on clinical samples compared to the BioFire FilmArray ME Panel. The PPA values observed for Haemophilus influenzae and Streptococcus pneumoniae were 80% and 88.24%, respectively. Negative percent agreement (NPA) values were >99.0% for each of the six bacterial targets and one fungal target tested with clinical samples. One viral target, herpes simplex virus 1, exhibited a PPA value of 100.0%, while the remaining viral targets-human parechovirus, herpes simplex virus 2, human herpes virus 6, and varicella zoster virus-were >90.0%, with the exception of enterovirus, which had a PPA value of 77.8%. The QIAstat-Dx ME Panel detected five true-positive and four true-negative cases compared to BioFire FilmArray ME Panel. The NPA values for all viral pathogens were >99.0%. Overall, the QIAstat-Dx ME Panel showed comparable performance to the BioFire FilmArray ME Panel as a rapid diagnostic tool for community-acquired meningitis and encephalitis.
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Affiliation(s)
- Thomas Sundelin
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev, Denmark
| | - Johanna Bialas
- Labor Berlin-Charite Vivantes Services GmbH, Berlin, Germany
| | - Juana de Diego
- Labor Berlin-Charite Vivantes Services GmbH, Berlin, Germany
| | | | - Hendrik Leibhan
- Labor Berlin-Charite Vivantes Services GmbH, Berlin, Germany
| | - Léa Ponderand
- Laboratoire de bactériologie, CHU Grenoble Alpes, La Tronche, France
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | | | - Melisa Rey
- STAT-Dx Life S.L. (a QIAGEN Company), Carrer de Baldiri Reixac, Barcelona, Spain
| | | | - Josep Pareja
- STAT-Dx Life S.L. (a QIAGEN Company), Carrer de Baldiri Reixac, Barcelona, Spain
| | - Yvan Caspar
- Laboratoire de bactériologie, CHU Grenoble Alpes, La Tronche, France
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
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Obaro S, Hassan-Hanga F, Medugu N, Olaosebikan R, Olanipekun G, Jibir B, Gambo S, Ajose T, Duru C, Ebruke B, Davies HD. Comparison of bacterial culture with BioFire® FilmArray® multiplex PCR screening of archived cerebrospinal fluid specimens from children with suspected bacterial meningitis in Nigeria. BMC Infect Dis 2023; 23:641. [PMID: 37784010 PMCID: PMC10544496 DOI: 10.1186/s12879-023-08645-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Diagnosis of bacterial meningitis remains a challenge in most developing countries due to low yield from bacterial culture, widespread use of non-prescription antibiotics, and weak microbiology laboratories. The objective of this study was to compare the yield from standard bacterial culture with the multiplex nested PCR platform, the BioFire® FilmArray® Meningitis/Encephalitis Panel (BioFire ME Panel), for cases with suspected acute bacterial meningitis. METHODS Following Gram stain and bacterial culture on cerebrospinal fluid (CSF) collected from children aged less than 5 years with a clinical suspicion of acute bacterial meningitis (ABM) as defined by the WHO guidelines, residual CSF specimens were frozen and later tested by BioFire ME Panel. RESULTS A total of 400 samples were analyzed. Thirty-two [32/400 (8%)] of the specimens were culture positive, consisting of; three Salmonella spp. (2 Typhi and 1 non-typhi), three alpha hemolytic Streptococcus, one Staphylococcus aureus, six Neisseria meningitidis, seven Hemophilus influenzae, 11 Streptococcus pneumoniae and 368 were culture negative. Of the 368 culture-negative specimens, the BioFire ME Panel detected at least one bacterial pathogen in 90 (24.5%) samples, consisting of S. pneumoniae, N. meningitidis and H. influenzae, predominantly. All culture positive specimens for H. influenzae, N. meningitidis and S. pneumoniae also tested positive with the BioFire ME Panel. In addition, 12 specimens had mixed bacterial pathogens identified. For the first time in this setting, we have data on the viral agents associated with meningitis. Single viral agents were detected in 11 (2.8%) samples while co-detections with bacterial agents or other viruses occurred in 23 (5.8%) of the samples. CONCLUSIONS The BioFire® ME Panel was more sensitive and rapid than culture for detecting bacterial pathogens in CSF. The BioFire® ME Panel also provided for the first time, the diagnosis of viral etiologic agents that are associated with meningoencephalitis in this setting. Institution of PCR diagnostics is recommended as a routine test for suspected cases of ABM to enhance early diagnosis and optimal treatment.
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Affiliation(s)
- S Obaro
- Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, NE, US
- International Foundation Against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
| | - F Hassan-Hanga
- Department of Pediatrics, Aminu Kano Teaching Hospital, Bayero University/ Bayero University, Kano, Nigeria
| | - N Medugu
- International Foundation Against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria.
- Department of Medical Microbiology and Immunology, Nile University of Nigeria, Abuja, Nigeria.
| | - R Olaosebikan
- Department of Pharmacology & Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, US
| | - G Olanipekun
- International Foundation Against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
| | - B Jibir
- Hasiya Bayero Pediatric Hospital, Kano, Nigeria
| | - S Gambo
- Department of Pediatrics, Murtala Mohammed Specialist Hospital, Kano, Nigeria
| | - Theresa Ajose
- International Foundation Against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
| | - Carissa Duru
- International Foundation Against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
| | - B Ebruke
- International Foundation Against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
| | - H D Davies
- Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, NE, US
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Wang H, Tomatis-Souverbielle C, Everhart K, Oyeniran SJ, Leber AL. Detection of human herpesvirus 6 in pediatric CSF samples: causing disease or incidental distraction? Diagn Microbiol Infect Dis 2023; 107:116029. [PMID: 37527599 DOI: 10.1016/j.diagmicrobio.2023.116029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 08/03/2023]
Abstract
Interpretation of human herpesvirus type 6 (HHV6) detection in the cerebrospinal fluid (CSF) of children can be complex; the virus can cause acute infection, reactivation, or can be inherited chromosomally integrated (iciHHV6). Our objectives were to determine the prevalence of HHV6 including iciHHV6 in CSF and compare the clinical and laboratory characteristics with and without iciHHV6 in our patient population. Overall, the prevalence of HHV6 and iciHHV6 was 2.4% and 0.85%, respectively. Children with iciHHV6 were significantly younger and less likely to present with fever. Septic infants (≤60 days) accounted for 65.2% (15/23) of the iciHHV6 patients. Patients with iciHHV6 had higher viral loads in CSF and whole blood. Twenty-one (91.3%) patients with iciHHV6 and 12 (33.3%) without ici-HHV6 were determined to have an incidental detection of HHV6 not associated with presenting symptoms. Molecular detection of HHV6 in CSF is not always associated with HHV6 infection and may represent iciHHV6 particularly in infants evaluated for sepsis.
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Affiliation(s)
- Huanyu Wang
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Cristina Tomatis-Souverbielle
- Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA
| | - Kathy Everhart
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Sophonie J Oyeniran
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Amy L Leber
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA; Department of Pathology, The Ohio State University, Columbus, OH, USA.
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Gaensbauer JT, Fernholz EC, Hiskey LM, Binnicker MJ, Corsini Campioli C. Comparison of two assays to diagnose herpes simplex virus in patients with central nervous system infections. J Clin Virol 2023; 166:105528. [PMID: 37390620 DOI: 10.1016/j.jcv.2023.105528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/02/2023]
Abstract
BACKGROUND Multiplex PCR panels are frequently used for detecting the diagnosis of central nervous system infection, but have demonstrated lower sensitivity for herpes simplex virus (HSV) compared to targeted PCRs. Providers in our institution frequently order both multiplex (BioFire Meningitis/Encephalitis Panel (MEP)) and targeted HSV PCR (Diasorin Simplexa HSV-1/2 Direct), allowing comparison of assay performance in practice and a unique clinical characterization of patients with concordant positive or discordant results. METHODS We retrospectively analyzed all HSV testing performed using the two assays simultaneously in a large multi-center institution between 12/10/2018 and 6/6/2022. We described and compared laboratory, diagnostic and therapeutic data between patients with positive results on both assays with patients with discordant results. RESULTS 1,387 patients were tested with both assays, of which 25 were positive on at least one assay. Eleven (44%) had discordant results; 9 were targeted-PCR-positive/MEP-negative and 2 were targeted-PCR-negative/MEP-positive. Compared with patients with concordant positive results, discordant targeted PCR-positive/MEP-negative patients had a higher PCR cycle threshold value (i.e., >35) and milder illness characterized by lower CSF WBC counts (4 vs 152; p = 0.032), fewer MRI abnormalities (37.5% vs. 87.5%; p = 0.039), HSV meningoencephalitis as primary discharge diagnosis (33% vs. 100%; p<0.0001) and were more often treated with oral medication or none at all. CONCLUSIONS Patients with discordant targeted PCR-positive/MEP-negative results represent a population with milder clinical disease. These findings will help clinicians and laboratorians determine when both targeted HSV and multiplex assays should be performed simultaneously and identify patients for whom a multiplex PCR may suffice, despite lower assay sensitivity.
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Affiliation(s)
- J T Gaensbauer
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Infectious Diseases, USA.
| | - E C Fernholz
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, USA
| | - L M Hiskey
- Department of Pediatric and Adolescent Medicine, Division of Pediatric Infectious Diseases, USA
| | - M J Binnicker
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, USA
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Ota K, Fujiwara S, Ishii J, Yoshimura H, Kohara N, Kawamoto M. [Efficacy of FilmArray ® ME panel for the rapid diagnosis of meningitis and encephalitis]. Rinsho Shinkeigaku 2023; 63:528-531. [PMID: 37518019 DOI: 10.5692/clinicalneurol.cn-001840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Microbial tests are essential for appropriate management for acute meningitis and encephalitis, but it often takes several days to identify the results of culture tests or PCR. BioFire FilmArray® meningitis/encephalitis panel (ME panel) is a rapid multiplex PCR assay that targets 14 bacteria, viruses, and yeast in 1 hour. In this single-center retrospective study, we reviewed adult patients who underwent ME panel test in parallel with conventional microbial tests from January to August 2021. Eighteen of 70 patients (26%) tested positive by ME panel, of which 8 patients (11%) were helpful in altering treatment strategy. Fifty-two patients (74%) could stop empirical treatment such as acyclovir or antibiotics due to negative results on ME panel. All results of ME panel were same as traditional assays. Use of ME panel can contribute to early diagnosis and treatment.
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Affiliation(s)
- Kazuma Ota
- Department of Neurology, Kobe City Medical Center General Hospital
| | - Satoru Fujiwara
- Department of Neurology, Kobe City Medical Center General Hospital
| | - Junko Ishii
- Department of Neurology, Kobe City Medical Center General Hospital
| | - Hajime Yoshimura
- Department of Neurology, Kobe City Medical Center General Hospital
| | - Nobuo Kohara
- Department of Neurology, Kobe City Medical Center General Hospital
| | - Michi Kawamoto
- Department of Neurology, Kobe City Medical Center General Hospital
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Romero-Hernández CA, Zuleta-Motta JL, Zapa-Pérez NM, Martínez-Lemus JD. [Experience with the Biofire FilmArray® for infectious meningitis/encephalitis in a high complexity institution in Bogota, Colombia]. Rev Neurol 2023; 77:87-93. [PMID: 37489856 PMCID: PMC10662192 DOI: 10.33588/rn.7704.2023082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 07/26/2023]
Abstract
INTRODUCTION Infectious meningoencephalitis (IME) is a neurological emergency with a significant rate of morbidity and mortality. The Biofire FilmArray® meningitis/encephalitis (FAME) panel for testing in cerebrospinal fluid (CSF) has proven to be a valuable tool for the aetiological diagnosis of IME, facilitating targeted antimicrobial therapy. The aim is to determine the impact of the FAME panel on antimicrobial therapeutic decisions in patients with suspected IME in the first 24 hours of clinical assessment. PATIENTS AND METHODS This is a descriptive observational study that comments on the clinical manifestations, the neuroimaging and paraclinical findings, and the antibiotic therapy of patients with suspected IME. An analysis was performed to determine the impact of FAME on antimicrobial therapy in the first 24 hours of the clinical assessment of patients. RESULTS Altogether 44 patients were included. The average time required to obtain the result of the FAME panel for testing in CSF was nine hours, with 20.4% (9/44) of tests yielding positive results. Within 24 hours of clinical assessment, their outcome had an impact on antimicrobial treatment decisions in 75% (33/44) of cases. In patients with a high clinical suspicion of IME, the result of FAME made it possible to change the initial empirical therapy to a targeted therapy in 15% (3/20) of cases and to discontinue the initial empirical therapy in 35% (7/20) of the subjects. In patients with low clinical suspicion of IME, their result allowed 25% (6/24) to have their suspicion confirmed and they were started on targeted antibiotic therapy; in contrast, 70.8% (17/24) had their diagnosis ruled out and were not started on treatment. CONCLUSIONS The result of the FAME panel for testing in CSF has a high impact on antimicrobial therapeutic decisions within 24 hours of clinical assessment. However, it must be interpreted with the clinical context, local epidemiology and other diagnostic studies.
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Affiliation(s)
- C A Romero-Hernández
- Fundación Cardioinfantil, Bogotá DC, Colombia
- Universidad Colegio Mayor de Nuestra Señora del Rosario, Bogotá DC, Colombia
| | - J L Zuleta-Motta
- Fundación Cardioinfantil, Bogotá DC, Colombia
- Universidad Colegio Mayor de Nuestra Señora del Rosario, Bogotá DC, Colombia
| | - N M Zapa-Pérez
- Fundación Cardioinfantil, Bogotá DC, Colombia
- Universidad Colegio Mayor de Nuestra Señora del Rosario, Bogotá DC, Colombia
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Fukushima S, Hagiya H, Yamamoto Y, Oguni K, Hasegawa K, Otsuka F. Cryptococcal Meningitis Developing in a Patient with Neurosarcoidosis. Intern Med 2023; 62:2433-2435. [PMID: 36575015 PMCID: PMC10484764 DOI: 10.2169/internalmedicine.0879-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/20/2022] [Indexed: 12/28/2022] Open
Abstract
Cryptococcal meningitis is a critical disease that occasionally involves immunosuppressed patients. We herein report a 79-year-old Japanese man who received low-dose prednisolone therapy for neurosarcoidosis and panhypopituitarism. He presented a 10-day history of a fever and altered mental status. The FilmArray® Meningitis/Encephalitis Panel and serum cryptococcal antigen tests were both negative, but the cerebrospinal fluid sample became positive for Cryptococcus neoformans after seven-day incubation. After the diagnosis of cryptococcal meningitis, we successfully treated the patient with a recommended treatment regimen. When an immunocompromised patient presents with a subacute fever accompanying any central nervous symptoms, cryptococcal meningitis should be screened for.
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Affiliation(s)
- Shinnosuke Fukushima
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan
| | - Hideharu Hagiya
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan
| | - Yukichika Yamamoto
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan
| | - Kohei Oguni
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan
| | - Kou Hasegawa
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan
| | - Fumio Otsuka
- Department of General Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Japan
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Holmen JE, Chung Thrash K, Donnelly B, Cruz G. A Neonate With Seizures. Pediatr Infect Dis J 2023; 42:730-732. [PMID: 37797323 DOI: 10.1097/inf.0000000000003893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Affiliation(s)
- Jenna E Holmen
- From the Department of Pediatrics, Division of Pediatric Infectious Disease, Santa Barbara Cottage Hospital, Santa Barbara, California
| | - Kathy Chung Thrash
- Department of Pediatrics, Division of Neonatology, Santa Barbara Cottage Hospital, Santa Barbara, California
| | - Barbara Donnelly
- Department of Pediatrics, Division of Neonatology, Santa Barbara Cottage Hospital, Santa Barbara, California
| | - Genevieve Cruz
- Department of Pediatrics, Division of Pediatric Neurology, Santa Barbara Cottage Hospital, Santa Barbara, California
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Yekani M, Memar MY. Immunologic biomarkers for bacterial meningitis. Clin Chim Acta 2023; 548:117470. [PMID: 37419301 DOI: 10.1016/j.cca.2023.117470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023]
Abstract
Meningitis is defined as the inflammation of the meninges that is most often caused by various bacterial and viral pathogens, and is associated with high rates of mortality and morbidity. Early detection of bacterial meningitis is essential to appropriate antibiotic therapy. Alterations in immunologic biomarkers levels have been considered the diagnostic approach in medical laboratories for the identifying of infections. The early increasing immunologic mediators such as cytokines and acute phase proteins (APPs) during bacterial meningitis have made they significant indicators for laboratory diagnosis. Immunology biomarkers showed wide variable sensitivity and specificity values that influenced by different reference values, selected a certain cutoff point, methods of detection, patient characterization and inclusion criteria, as well as etiology of meningitis and time of CSF or blood specimens' collection. This study provides an overview of different immunologic biomarkers as diagnostic markers for the identification of bacterial meningitis and their efficiencies in the differentiating of bacterial from viral meningitis.
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Affiliation(s)
- Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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van der Hoeven A, van der Beek MT, Bekker V, Meijers E, Ivens MJR, Wessels E, Kroes ACM, Boers SA. Improved Diagnostics in Bacterial Neonatal Meningitis Using a Next-Generation Sequencing Platform. Infect Dis Ther 2023:10.1007/s40121-023-00844-8. [PMID: 37436676 PMCID: PMC10390448 DOI: 10.1007/s40121-023-00844-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
INTRODUCTION Bacterial meningitis in infants is an infrequent but life-threatening condition. Empiric therapy should begin as soon as meningitis is thought likely. Consequently, the causative microorganisms may not always be detected using culturing techniques, as cerebrospinal fluid (CSF) cultures are influenced by antibiotics. Nucleic acid amplification tests, such as polymerase chain reaction (PCR) (multiplex panels), may overcome this limitation but require a priori knowledge of the likely pathogen present within the sample. With this in mind, we investigated to what extent a culture-free, broad-range 16S rRNA gene next-generation sequencing (NGS) platform (MYcrobiota) could add to the microbiological diagnosis of meningitis. METHODS Retrospective cohort study at level III neonatal intensive care unit. Included were all infants with suspected meningitis admitted between 10 November 2017 and 31 December 2020. A comparison was made of the bacterial pathogen detection rate between MYcrobiota and conventional bacterial culture. RESULTS In a 3-year period, 37 CSF samples (diagnostic and follow-up) from 35 infants with proven or possible meningitis were available for MYcrobiota testing. MYcrobiota detected the presence of bacterial pathogens in 11 samples (30%), in contrast with the conventional CSF culture, which detected bacteria in 2 of 36 samples (5.6%). CONCLUSION Addition of 16S rRNA sequencing to conventional culturing greatly improved the identification of the aetiology of bacterial meningitis compared to culturing of CSF samples alone.
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Affiliation(s)
- Alieke van der Hoeven
- Department of Medical Microbiology, Leiden University Medical Center, Postzone E4-P, Postbus 9600, 2300 RC, Leiden, The Netherlands.
| | - Martha T van der Beek
- Department of Medical Microbiology, Leiden University Medical Center, Postzone E4-P, Postbus 9600, 2300 RC, Leiden, The Netherlands
| | - Vincent Bekker
- Division of Neonatology, Department of Paediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Erin Meijers
- Department of Medical Microbiology, Leiden University Medical Center, Postzone E4-P, Postbus 9600, 2300 RC, Leiden, The Netherlands
| | - Marco J R Ivens
- Department of Medical Microbiology, Leiden University Medical Center, Postzone E4-P, Postbus 9600, 2300 RC, Leiden, The Netherlands
| | - Els Wessels
- Department of Medical Microbiology, Leiden University Medical Center, Postzone E4-P, Postbus 9600, 2300 RC, Leiden, The Netherlands
| | - Aloysius C M Kroes
- Department of Medical Microbiology, Leiden University Medical Center, Postzone E4-P, Postbus 9600, 2300 RC, Leiden, The Netherlands
| | - Stefan A Boers
- Department of Medical Microbiology, Leiden University Medical Center, Postzone E4-P, Postbus 9600, 2300 RC, Leiden, The Netherlands.
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Mizusawa M, Carroll KC. Recent updates in the development of molecular assays for the rapid identification and susceptibility testing of MRSA. Expert Rev Mol Diagn 2023; 23:679-699. [PMID: 37419696 DOI: 10.1080/14737159.2023.2234823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/22/2023] [Accepted: 07/06/2023] [Indexed: 07/09/2023]
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of healthcare- and community-associated infections. Nasal carriage of MRSA is a risk factor for subsequent MRSA infections. Increased morbidity and mortality are associated with MRSA infections and screening and diagnostic tests for MRSA play an important role in clinical management. AREAS COVERED A literature search was conducted in PubMed and supplemented by citation searching. In this article, we provide a comprehensive review of molecular-based methods for MRSA screening and diagnostic tests including individual nucleic acid detection assays, syndromic panels, and sequencing technologies with a focus on their analytical performance. EXPERT OPINION Molecular based-assays for the detection of MRSA have improved in terms of accuracy and availability. Rapid turnaround enables earlier contact isolation and decolonization for MRSA. The availability of syndromic panel tests that include MRSA as a target has expanded from positive blood cultures to pneumonia and osteoarticular infections. Sequencing technologies allow detailed characterizations of novel methicillin-resistance mechanisms that can be incorporated into future assays. Next generation sequencing is capable of diagnosing MRSA infections that cannot be identified by conventional methods and metagenomic next-generation sequencing (mNGS) assays will likely move closer to implementation as front-line diagnostics in the near future.
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Affiliation(s)
- Masako Mizusawa
- Monmouth Medical Center, Rutgers University Robert Wood Johnson Medical School, Long Branch, NJ, USA
| | - Karen C Carroll
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Humisto A, Antikainen J, Holma T, Jarva H, Toivonen A, Loginov R, Mannonen L. Evaluation of the Novel CE-IVD-Marked Multiplex PCR QIAstat-Dx Meningitis/Encephalitis Panel. Microbiol Spectr 2023; 11:e0514422. [PMID: 37042772 PMCID: PMC10269741 DOI: 10.1128/spectrum.05144-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/23/2023] [Indexed: 04/13/2023] Open
Abstract
Central nervous system (CNS) infections such as meningitis and encephalitis are life-threatening conditions that demand hospital care and prompt identification of the causative agent. Since 2015, there has been only one CE-IVD-marked rapid multiplexed diagnostic assay in cassette format for bacterial and viral detection from cerebrospinal fluid (CSF): the BioFire FilmArray meningitis/encephalitis (ME) panel. In the beginning of 2022, Qiagen introduced the QIAstat-Dx meningitis/encephalitis panel. It is a CE-IVD-marked multiplex PCR cassette test intended for the identification of suspected infectious meningitis, encephalitis, or meningoencephalitis caused by bacterial, viral, or fungal pathogens. In this study, we evaluated patient and quality control samples using the QIAstat-Dx meningitis/encephalitis panel and compared the results to those of the BioFire FilmArray meningitis/encephalitis panel and reference methods (current routine analysis methods in our laboratory, PCR, or cultivation). The combined positive percent agreement between the two panel assays was 100%, and the negative percent agreement was 94%. We further compared specifically herpes simplex virus 1 (HSV-1), HSV-2, and varicella-zoster virus (VZV) dilution series using six commercial herpesvirus assays, including the two cassette tests. The results suggested that real-time PCR methods (with separate extraction) were the most sensitive methods. When comparing the cassette tests, the BioFire FilmArray meningitis/encephalitis panel produced more positive results than the QIAstat-Dx meningitis/encephalitis panel in the herpesvirus analyses. IMPORTANCE The diagnosis of infectious meningitis and encephalitis relies mostly on specific PCR and culturing methods, but commercial syndromic panel assays are bringing a change in diagnostics. With multiplexed analysis, the identification of the pathogen is potentially faster, and less sample material is needed. The novel QIAstat-Dx meningitis/encephalitis panel assay is intended for the rapid identification of pathogens from cerebrospinal fluid for suspected central nervous system (CNS) infection, which is a life-threatening condition and difficult to diagnose. We studied the performance of this panel assay using patient samples and dilution series of selected viruses. The evaluation data for this novel meningitis/encephalitis panel assay are useful for other clinical laboratories and organizations using or considering using this test.
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Affiliation(s)
- Anu Humisto
- Department of Clinical Microbiology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Jenni Antikainen
- Department of Clinical Microbiology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Tanja Holma
- Department of Clinical Microbiology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Hanna Jarva
- Department of Clinical Microbiology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Anne Toivonen
- Department of Clinical Microbiology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Raisa Loginov
- Department of Clinical Microbiology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Laura Mannonen
- Department of Clinical Microbiology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
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Tomatis Souverbielle C, Erdem G, Sánchez PJ. Update on nonpolio enterovirus and parechovirus infections in neonates and young infants. Curr Opin Pediatr 2023; 35:380-389. [PMID: 36876331 DOI: 10.1097/mop.0000000000001236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
PURPOSE OF REVIEW To review the epidemiology, clinical manifestations, and treatment strategies of nonpolio enterovirus and parechovirus (PeV) infections, and identify research gaps. RECENT FINDINGS There is currently no approved antiviral agent for enterovirus or PeV infections, although pocapavir may be provided on a compassionate basis. Elucidation of the structure and functional features of enterovirus and PeV may lead to novel therapeutic strategies, including vaccine development. SUMMARY Nonpolio human enterovirus and PeV are common childhood infections that are most severe among neonates and young infants. Although most infections are asymptomatic, severe disease resulting in substantial morbidity and mortality occurs worldwide and has been associated with local outbreaks. Long-term sequelae are not well understood but have been reported following neonatal infection of the central nervous system. The lack of antiviral treatment and effective vaccines highlight important knowledge gaps. Active surveillance ultimately may inform preventive strategies.
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Affiliation(s)
| | - Guliz Erdem
- Department of Pediatrics, Section of Infectious Diseases
| | - Pablo J Sánchez
- Department of Pediatrics, Section of Infectious Diseases
- Division of Neonatology, Department of Pediatrics, Nationwide Children's Hospital, Abigail Wexner Research Institute at Nationwide Children's Hospital, Center for Perinatal Research, The Ohio State University College of Medicine, Columbus, Ohio, USA
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Marsh MC, Lin HM, Black J, Allen K, Weiner B, Ramilo O, Klamer B, Watson JR, Kasick R. Preterm and Term Infants Evaluated for Sepsis: Differences in Management and Clinical Outcomes. Hosp Pediatr 2023; 13:544-554. [PMID: 37222075 DOI: 10.1542/hpeds.2022-007050] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND OBJECTIVES To describe differences in practice patterns and outcomes of young preterm versus age-matched term infants evaluated for sepsis, because evaluation and management of this group are not well defined. METHODS We conducted a retrospective single-center study at an academic, freestanding children's hospital of previously healthy preterm and term infants aged 0 to 60 days, who presented for initial evaluation of fever and/or hypothermia from 2014 to 2019. We classified infants by gestational age as preterm (32-36 6/7 weeks) and term (37-42 weeks) and compared diagnostic evaluation, management, and clinical outcomes. RESULTS Out of 363 preterm infants evaluated for sepsis, 336 met inclusion criteria; within the same study period, 2331 term infants were evaluated for sepsis, of which 600 were randomly selected and 554 were included. Clinicians performed inflammatory marker testing and chest x-rays more frequently in preterm infants 31% vs 25% (P = .034) and 50% vs 32% (P < .001), respectively. Preterm infants had a higher rate of bacteremia 5.9% vs 2.5% (P = .035), were hospitalized more frequently 72% vs 63% (P = .006), and required ICU level of care more often 32% vs 5% (P < .001) than term infants. They had lower rates of viral infections 33% vs 42% (P = .015) and no significant increased return visits. Febrile preterm and term infants, and older hypothermic preterm infants had relatively higher rates of serious bacterial infections. Hypothermic preterm infants had the longest hospitalizations. CONCLUSIONS Preterm infants had increased rates of bacteremia and required higher level of care compared with age-matched term infants, likely reflecting their increased risk for sepsis and other concomitant morbidities associated with preterm birth.
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Affiliation(s)
| | | | - Joshua Black
- Nationwide Children's Hospital, Columbus, Ohio
- The Ohio State University, College of Medicine, Columbus, Ohio
| | - Karen Allen
- Nationwide Children's Hospital, Columbus, Ohio
| | - Benjamin Weiner
- The Ohio State University, College of Medicine, Columbus, Ohio
| | - Octavio Ramilo
- Nationwide Children's Hospital, Columbus, Ohio
- The Ohio State University, College of Medicine, Columbus, Ohio
| | - Brett Klamer
- Nationwide Children's Hospital, Columbus, Ohio
- The Ohio State University, College of Medicine, Columbus, Ohio
| | - Joshua R Watson
- Nationwide Children's Hospital, Columbus, Ohio
- The Ohio State University, College of Medicine, Columbus, Ohio
| | - Rena Kasick
- Nationwide Children's Hospital, Columbus, Ohio
- The Ohio State University, College of Medicine, Columbus, Ohio
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Yong HYF, Pastula DM, Kapadia RK. Diagnosing viral encephalitis and emerging concepts. Curr Opin Neurol 2023; 36:175-184. [PMID: 37078655 DOI: 10.1097/wco.0000000000001155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
PURPOSE OF REVIEW This review offers a contemporary clinical approach to the diagnosis of viral encephalitis and discusses recent advances in the field. The neurologic effects of coronaviruses, including COVID-19, as well as management of encephalitis are not covered in this review. RECENT FINDINGS The diagnostic tools for evaluating patients with viral encephalitis are evolving quickly. Multiplex PCR panels are now in widespread use and allow for rapid pathogen detection and potentially reduce empiric antimicrobial exposure in certain patients, while metagenomic next-generation sequencing holds great promise in diagnosing challenging and rarer causes of viral encephalitis. We also review topical and emerging infections pertinent to neuroinfectious disease practice, including emerging arboviruses, monkeypox virus (mpox), and measles. SUMMARY Although etiological diagnosis remains challenging in viral encephalitis, recent advances may soon provide the clinician with additional tools. Environmental changes, host factors (such as ubiquitous use of immunosuppression), and societal trends (re-emergence of vaccine preventable diseases) are likely to change the landscape of neurologic infections that are considered and treated in clinical practice.
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Affiliation(s)
- Heather Y F Yong
- Division of Neurology, Department of Clinical Neurosciences, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada
| | - Daniel M Pastula
- Neuro-Infectious Diseases Group, Department of Neurology and Division of Infectious Diseases, University of Colorado School of Medicine
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Ronak K Kapadia
- Division of Neurology, Department of Clinical Neurosciences, University of Calgary, Cummings School of Medicine, Calgary, Alberta, Canada
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Tan HJ, Shahren AAH, Khoo CS, Ng CF, Zaidi WAW, Kori N, Periyasamy P, Eu CL, Payus AO, Hod R. Anxiety among hospitalized COVID-19 patients: a case-control study from a tertiary teaching hospital in Malaysia. Front Psychiatry 2023; 14:1148019. [PMID: 37275980 PMCID: PMC10232945 DOI: 10.3389/fpsyt.2023.1148019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/27/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Anxiety has been increasingly recognized as part of the psychosocial health issues in COVID-19 patients. However, the impact of this topic may be underestimated in low- and middle-income countries. This study aimed to estimate the prevalence of and risk factors of anxiety in COVID-19 patients compared to controls in a local tertiary teaching hospital in Malaysia. Methods In this case-control study, we analyzed data on adult patients aged 18 years and above hospitalized for COVID-19 infection with matched hospitalized controls. The demographic, clinical data and anxiety measures using the Generalized Anxiety Disorder-7 questionnaire were analyzed using univariate and multivariate analysis. Results 86.6% in the COVID-19 group had anxiety, significantly higher than 13.4% in the control group (p = 0.001). The COVID-19 group was significantly associated with the GAD-7 severity (p = 0.001). The number of COVID-19 patients in the mild, moderate, and severe anxiety groups was 48 (84.2%), 37 (86%), and 18 (94.7%), respectively. Multiple logistic regression showed significant predictors for anxiety, including COVID-19 diagnosis and neurological symptoms. Anxiety was found 36.92 times higher in the patients with COVID-19 compared to those without COVID-19 (OR 36.92;95% CI 17.09, 79.78, p = 0.001). Patients with neurological symptoms were at risk of having anxiety (OR 2.94; 95% CI 1.03, 8.41, p = 0.044). Discussion COVID-19 patients experience a significant disruption in psychosocial functioning due to hospitalization. The burden of anxiety is notably high, compounded by a diagnosis of COVID-19 itself and neurological symptomatology. Early psychiatric referrals are warranted for patients at risk of developing anxiety symptoms.
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Affiliation(s)
- Hui Jan Tan
- Department of Medicine, Faculty of Medicine, The National University of Malaysia, Kuala Lumpur, Malaysia
| | - Abdool Alleem Hj Shahren
- Department of Medicine, Faculty of Medicine, The National University of Malaysia, Kuala Lumpur, Malaysia
| | - Ching Soong Khoo
- Department of Medicine, Faculty of Medicine, The National University of Malaysia, Kuala Lumpur, Malaysia
| | - Chen Fei Ng
- Department of Medicine, Faculty of Medicine, The National University of Malaysia, Kuala Lumpur, Malaysia
| | - Wan Asyraf Wan Zaidi
- Department of Medicine, Faculty of Medicine, The National University of Malaysia, Kuala Lumpur, Malaysia
| | - Najma Kori
- Department of Medicine, Faculty of Medicine, The National University of Malaysia, Kuala Lumpur, Malaysia
| | - Petrick Periyasamy
- Department of Medicine, Faculty of Medicine, The National University of Malaysia, Kuala Lumpur, Malaysia
| | - Choon Leng Eu
- Department of Psychiatry, Faculty of Medicine, The National University of Malaysia, Kuala Lumpur, Malaysia
| | - Alvin Oliver Payus
- Department of Medicine, Faculty of Medicine, University Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Rozita Hod
- Department of Community Health, Faculty of Medicine, The National University of Malaysia, Kuala Lumpur, Malaysia
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Escamilla JE, January SE, Vazquez Guillamet R. Diagnosis and Treatment of Fungal Infections in Lung Transplant Recipients. Pathogens 2023; 12:pathogens12050694. [PMID: 37242364 DOI: 10.3390/pathogens12050694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/27/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Fungal infections are a significant source of morbidity in the lung transplant population via direct allograft damage and predisposing patients to the development of chronic lung allograft dysfunction. Prompt diagnosis and treatment are imperative to limit allograft damage. This review article discusses incidence, risk factors, and symptoms with a specific focus on diagnostic and treatment strategies in the lung transplant population for fungal infections caused by Aspergillus, Candida, Coccidioides, Histoplasma, Blastomyces, Scedosporium/Lomentospora, Fusarium, and Pneumocystis jirovecii. Evidence for the use of newer triazole and inhaled antifungals to treat isolated pulmonary fungal infections in lung transplant recipients is also discussed.
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Affiliation(s)
- Jesus E Escamilla
- Department of Pharmacy, Barnes-Jewish Hospital, Saint Louis, MO 63110, USA
| | - Spenser E January
- Department of Pharmacy, Barnes-Jewish Hospital, Saint Louis, MO 63110, USA
| | - Rodrigo Vazquez Guillamet
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Rodrigo Vazquez Guillamet, 4921 Parkview Place, Saint Louis, MO 63110, USA
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45
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Berkhout A, Cheng DR, McNab S, Lee LY, Daley AJ, Clifford V. Clinical and Health System Impact of Biofire Filmarray Meningitis/Encephalitis Routine Testing of CSF in a Pediatric Hospital: An Observational Study. Pediatr Infect Dis J 2023; 42:281-285. [PMID: 36728816 DOI: 10.1097/inf.0000000000003812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Rapid cartridge-based molecular test panels targeting multiple pathogens are increasingly available, improve pathogen detection and reduce turn-around-time but are more expensive than standard testing. Confirmation that these test panels contribute to improved patient or health service outcomes is required. METHODS In March 2021, our pediatric hospital laboratory implemented the BioFire Filmarray™ meningitis/encephalitis (M/E) panel as an additional routine test for all cerebrospinal fluid (CSF) samples collected from infants <90 days or from any patient in the emergency department. A retrospective chart review was done to ascertain changes in clinical outcomes, antimicrobial prescribing practices, and hospital length of stay, comparing two discrete 6-month periods: preimplementation (March-August 2019) and postimplementation (March-August 2021). RESULTS Both pre- and postimplementation groups were similar at baseline, except the preimplementation group had a higher proportion of infants with enterovirus and parechovirus meningitis. There was no significant difference between the groups in terms of median length of stay (2.94 vs 3.47 days, p = 0.41), duration of antibiotic treatment (2.0 vs 2.3 days, p = 0.25), need for central venous access (12.9% vs 17%, p = 0.38) or hospital-in-the-home admission (9.4% vs 9%, p = 0.92). A similar proportion of infants received aciclovir (33% vs 31%), however, a reduction in duration was observed (1.36 vs 0.90 days, p = 0.03) in the postimplementation period. CONCLUSIONS Introduction of the Biofire Filmarray™ M/E panel for routine testing of CSF samples reduced the duration of antiviral prescribing but had only a minor impact on antibiotic prescribing practices or health service outcomes in our pediatric hospital. The introduction of new laboratory testing needs to be supported by a comprehensive stewardship program to see optimal outcomes from new testing platforms.
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Affiliation(s)
- Angela Berkhout
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
- Infection Management & Prevention Service, The Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Daryl R Cheng
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
| | - Sarah McNab
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
| | - Lai-Yang Lee
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Andrew J Daley
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
| | - Vanessa Clifford
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- General Medicine, Royal Children's Hospital, Parkville, Victoria, Australia
- The University of Queensland, Faculty of Medicine, Brisbane. Queensland, Australia
- Department of Paediatrics, University of Melbourne, Victoria, Australia
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Ngo Nsoga MT, Pérez-Rodriguez FJ, Mamin A, L’Huillier AG, Cherkaoui A, Kaiser L, Schibler M. Rational Use of Microbiological Tests in the Diagnosis of Central Nervous System Infections Using Restrictive Criteria: a Retrospective Study. Microbiol Spectr 2023:e0317922. [PMID: 36971564 PMCID: PMC10100671 DOI: 10.1128/spectrum.03179-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Microbiological testing in general and in the setting of central nervous system (CNS) infection in particular are often excessive, leading to superfluous laboratory work and costs. In this regard, restrictive criteria, named Reller criteria, have been developed to reduce unnecessary CSF herpes simplex virus 1 (HSV-1) PCR testing when suspecting encephalitis.
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47
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Galardi MM, Sowa GM, Crockett CD, Rudock R, Smith AE, Shwe EE, San T, Linn K, Aye AMM, Ramachandran PS, Zia M, Wapniarski AE, Hawes IA, Hlaing CS, Kyu EH, Thair C, Mar YY, Nway N, Storch GA, Wylie KM, Wylie TN, Dalmau J, Wilson MR, Mar SS. Pathogen and Antibody Identification in Children with Encephalitis in Myanmar. Ann Neurol 2023; 93:615-628. [PMID: 36443898 DOI: 10.1002/ana.26560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/22/2022] [Accepted: 11/20/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Prospective studies of encephalitis are rare in regions where encephalitis is prevalent, such as low middle-income Southeast Asian countries. We compared the diagnostic yield of local and advanced tests in cases of pediatric encephalitis in Myanmar. METHODS Children with suspected subacute or acute encephalitis at Yangon Children's Hospital, Yangon, Myanmar, were prospectively recruited from 2016-2018. Cohort 1 (n = 65) had locally available diagnostic testing, whereas cohort 2 (n = 38) had advanced tests for autoantibodies (ie, cell-based assays, tissue immunostaining, studies with cultured neurons) and infections (ie, BioFire FilmArray multiplex Meningitis/Encephalitis multiplex PCR panel, metagenomic sequencing, and pan-viral serologic testing [VirScan] of cerebrospinal fluid). RESULTS A total of 20 cases (13 in cohort 1 and 7 in cohort 2) were found to have illnesses other than encephalitis. Of the 52 remaining cases in cohort 1, 43 (83%) had presumed infectious encephalitis, of which 2 cases (4%) had a confirmed infectious etiology. Nine cases (17%) had presumed autoimmune encephalitis. Of the 31 cases in cohort 2, 23 (74%) had presumed infectious encephalitis, of which one (3%) had confirmed infectious etiology using local tests only, whereas 8 (26%) had presumed autoimmune encephalitis. Advanced tests confirmed an additional 10 (32%) infections, 4 (13%) possible infections, and 5 (16%) cases of N-methyl-D-aspartate receptor antibody encephalitis. INTERPRETATION Pediatric encephalitis is prevalent in Myanmar, and advanced technologies increase identification of treatable infectious and autoimmune causes. Developing affordable advanced tests to use globally represents a high clinical and research priority to improve the diagnosis and prognosis of encephalitis. ANN NEUROL 2023;93:615-628.
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Affiliation(s)
- Maria M Galardi
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Gavin M Sowa
- Department of Medicine, McGaw Medical Center of Northwestern University, Chicago, IL
| | - Cameron D Crockett
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Robert Rudock
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Alyssa E Smith
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Ei E Shwe
- Department of Pathology, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Thidar San
- Department of Pathology, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Kyaw Linn
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Aye Mya M Aye
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Prashanth S Ramachandran
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Maham Zia
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Anne E Wapniarski
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Isobel A Hawes
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Chaw S Hlaing
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Ei H Kyu
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Cho Thair
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Yi Y Mar
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Nway Nway
- Department of Pediatrics, Yangon Children's Hospital, Institute of Medicine 1, Yangon, Myanmar
| | - Gregory A Storch
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Kristine M Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Todd N Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | - Josep Dalmau
- Neuroimmunology Program, Institut d'Investigacions Biomèdiques August Pi i Sunyer Hospital Clínic, University of Barcelona, Barcelona, Spain.,Department of Neurology, University of Pennsylvania, Philadelphia, PA.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Michael R Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Soe S Mar
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
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Völk S, Dobler F, Koedel U, Pfister HW, Bruegel M, Schubert S, Klein M. Cerebrospinal fluid analysis in emergency patients with suspected infection of the central nervous system. Eur J Neurol 2023; 30:702-709. [PMID: 36398479 DOI: 10.1111/ene.15638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND AND PURPOSE Meningitis and encephalitis are potentially life-threatening diseases that require fast and accurate diagnostics and therapy. The value of polymerase chain reaction (PCR) multiplex testing in clinical practice is still a matter of debate. This study aims to evaluate its benefits and limitations in emergency patients. METHODS We assessed the value of a meningoencephalitis PCR array in the clinical routine of an emergency department. RESULTS Of 1578 emergency patients who received a lumbar puncture, 43% received it for a clinically suspected central nervous system (CNS) infection. After initial workup for cerebrospinal fluid (CSF) cell count, protein and glucose, a CNS infection was still considered likely in 307 patients. In these patients, further microbiologic workup was performed. A total of 230 samples were examined by PCR and a pathogen was detected in 66 of these samples. In the case of a positive microbiologic result, a comparison between PCR array and standard method was available for 59 samples, which demonstrated an overcall agreement of 80% (n = 47/59). Of interest, exclusively array-positive results were observed for patients with meningitis found to be positive for Streptococcus pneumoniae; four out of five patients had been treated with antibiotics before the lumbar puncture. In samples with normal CSF cell count only two positive array results were obtained, both for human herpesvirus 6, and these were not clinically relevant. CONCLUSION Our data suggest that the array substantially contributes to a detection of pathogens in patients with suspected CNS infection and seems of particular interest in patients with acute bacterial meningitis under empiric antibiotic treatment. In CSF samples with normal cell count, it might be dispensable.
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Affiliation(s)
- Stefanie Völk
- Department of Neurology, University Hospital, LMU, Munich, Germany
| | - Fabian Dobler
- Department of Neurology, University Hospital, LMU, Munich, Germany
| | - Uwe Koedel
- Department of Neurology, University Hospital, LMU, Munich, Germany
| | | | - Mathias Bruegel
- Institute of Laboratory Medicine, University Hospital, LMU, Munich, Germany
| | - Sören Schubert
- Max von Pettenkofer-Institute, Faculty of Medicine, LMU, Munich, Germany
| | - Matthias Klein
- Department of Neurology, University Hospital, LMU, Munich, Germany
- Emergency Department, University Hospital, LMU, Munich, Germany
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Parker K, Wood H, Russell JA, Yarmosh D, Shteyman A, Bagnoli J, Knight B, Aspinwall JR, Jacobs J, Werking K, Winegar R. Development and Optimization of an Unbiased, Metagenomics-Based Pathogen Detection Workflow for Infectious Disease and Biosurveillance Applications. Trop Med Infect Dis 2023; 8:tropicalmed8020121. [PMID: 36828537 PMCID: PMC9966482 DOI: 10.3390/tropicalmed8020121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/25/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Rapid, specific, and sensitive identification of microbial pathogens is critical to infectious disease diagnosis and surveillance. Classical culture-based methods can be applied to a broad range of pathogens but have long turnaround times. Molecular methods, such as PCR, are time-effective but are not comprehensive and may not detect novel strains. Metagenomic shotgun next-generation sequencing (NGS) promises specific identification and characterization of any pathogen (viruses, bacteria, fungi, and protozoa) in a less biased way. Despite its great potential, NGS has yet to be widely adopted by clinical microbiology laboratories due in part to the absence of standardized workflows. Here, we describe a sample-to-answer workflow called PanGIA (Pan-Genomics for Infectious Agents) that includes simplified, standardized wet-lab procedures and data analysis with an easy-to-use bioinformatics tool. PanGIA is an end-to-end, multi-use workflow that can be used for pathogen detection and related applications, such as biosurveillance and biothreat detection. We performed a comprehensive survey and assessment of current, commercially available wet-lab technologies and open-source bioinformatics tools for each workflow component. The workflow includes total nucleic acid extraction from clinical human whole blood and environmental microbial forensic swabs as sample inputs, host nucleic acid depletion, dual DNA and RNA library preparation, shotgun sequencing on an Illumina MiSeq, and sequencing data analysis. The PanGIA workflow can be completed within 24 h and is currently compatible with bacteria and viruses. Here, we present data from the development and application of the clinical and environmental workflows, enabling the specific detection of pathogens associated with bloodstream infections and environmental biosurveillance, without the need for targeted assay development.
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Affiliation(s)
- Kyle Parker
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
- Correspondence: (K.P.); (R.W.)
| | - Hillary Wood
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
| | | | - David Yarmosh
- MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD 20850, USA
| | - Alan Shteyman
- MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD 20850, USA
| | - John Bagnoli
- MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD 20850, USA
| | - Brittany Knight
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
| | - Jacob R. Aspinwall
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
| | - Jonathan Jacobs
- MRIGlobal, 65 West Watkins Mill Road, Gaithersburg, MD 20850, USA
| | - Kristine Werking
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
| | - Richard Winegar
- MRIGlobal, 425 Dr. Martin Luther King Jr. Blvd, Kansas City, MO 64110, USA
- Correspondence: (K.P.); (R.W.)
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50
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Barichello T, Rocha Catalão CH, Rohlwink UK, van der Kuip M, Zaharie D, Solomons RS, van Toorn R, Tutu van Furth M, Hasbun R, Iovino F, Namale VS. Bacterial meningitis in Africa. Front Neurol 2023; 14:822575. [PMID: 36864913 PMCID: PMC9972001 DOI: 10.3389/fneur.2023.822575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/18/2023] [Indexed: 02/16/2023] Open
Abstract
Bacterial meningitis differs globally, and the incidence and case fatality rates vary by region, country, pathogen, and age group; being a life-threatening disease with a high case fatality rate and long-term complications in low-income countries. Africa has the most significant prevalence of bacterial meningitis illness, and the outbreaks typically vary with the season and the geographic location, with a high incidence in the meningitis belt of the sub-Saharan area from Senegal to Ethiopia. Streptococcus pneumoniae (pneumococcus) and Neisseria meningitidis (meningococcus) are the main etiological agents of bacterial meningitis in adults and children above the age of one. Streptococcus agalactiae (group B Streptococcus), Escherichia coli, and Staphylococcus aureus are neonatal meningitis's most common causal agents. Despite efforts to vaccinate against the most common causes of bacterial neuro-infections, bacterial meningitis remains a significant cause of mortality and morbidity in Africa, with children below 5 years bearing the heaviest disease burden. The factors attributed to this continued high disease burden include poor infrastructure, continued war, instability, and difficulty in diagnosis of bacterial neuro-infections leading to delay in treatment and hence high morbidity. Despite having the highest disease burden, there is a paucity of African data on bacterial meningitis. In this article, we discuss the common etiologies of bacterial neuroinfectious diseases, diagnosis and the interplay between microorganisms and the immune system, and the value of neuroimmune changes in diagnostics and therapeutics.
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Affiliation(s)
- Tatiana Barichello
- Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
- Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Carlos Henrique Rocha Catalão
- Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Department of Neuroscience and Behavioral Science, Ribeirao Preto Medical School, University of São Paulo (USP), Ribeirao Preto, SP, Brazil
| | - Ursula K. Rohlwink
- Pediatric Neurosurgery Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- Division of Neurosurgery, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Martijn van der Kuip
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, Netherlands
| | - Dan Zaharie
- Department of Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Services, Tygerberg Hospital, Cape Town, South Africa
| | - Regan S. Solomons
- Department of Pediatric and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ronald van Toorn
- Department of Pediatric and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Marceline Tutu van Furth
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, Vrije Universiteit, Amsterdam, Netherlands
| | - Rodrigo Hasbun
- Division of Infectious Diseases, Department of Internal Medicine, UT Health, McGovern Medical School, Houston, TX, United States
| | - Federico Iovino
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Vivian Ssonko Namale
- Columbia University Irving Medical Center and New York Presbyterian Hospital, New York, NY, United States
- Department of Paediatrics and Child Health, Makerere University College of Health Sciences, Kampala, Uganda
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