1
|
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.
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Wang C, Xu H, Liu G, Liu J, Yu H, Chen B, Zheng G, Shu M, Du L, Xu Z, Huang L, Li H, Shu S, Chen Y. A Multicenter Epidemiological and Pathogenic Characteristics Study of Community-Acquired Bacterial Meningitis Children in China: Results from the Chinese Pediatric Bacterial Meningitis Surveillance (CPBMS) 2019-2020. Infect Drug Resist 2023; 16:6587-6601. [PMID: 37849791 PMCID: PMC10577658 DOI: 10.2147/idr.s413147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/25/2023] [Indexed: 10/19/2023] Open
Abstract
Objective To explore the epidemiological and pathogenic characteristics of children with community-acquired bacterial meningitis. Methods A multicenter, retrospective study was conducted among CABM patients under 15 years old from 33 hospitals in China from 2019 to 2020. The medical record, laboratory, and microbiological data were collected and analyzed. Results A total of 1610 children with CABM were identified and presented at a median onset age of 45 days of whom 955 (59.3%) were males. CABM occurred mostly in infants <1 year of age (84.0%, 1352/1610). In etiology-confirmed cases, the pathogens were isolated from CSF culture in 515 (32.0%), 400 (24.8%) in blood culture, and 186 (11.6%) both in CSF and blood culture. In total, 126 pathogens were identified through CSF mNGS in 330 CABM cases; 21 S. pneumoniae isolates were detected in 83 CABM cases by antigen detection method. Major pathogens were E. coli (195, 24.7%), GBS (170, 21.5%), and S. pneumoniae (157, 19.9%). GBS (29.3%, 22/75) was the first pathogen of CABM in neonates aged 0-6 days old, while E. coli (44.7%, 76/170) in 7 to 28 days of age; S. pneumoniae (96.2%, 151/157) was the most common pathogen in >3 months old cases. About 9.7% (19/195) strains of E. coli produced ultra‑broad‑spectrum β‑lactamases. The common intracranial imaging complications were subdural effusion and (or) empyema in 349 (21.7%), hydrocephalus in 233 (14.5%), and cerebral abscess in 178 (11.1%). A total of 389 (24.2%) cases were completely cured and 1088 (67.6%) cases improved. Among 166 patients (10.3%) with adverse outcomes, 32 cases (2.0%) died, and 37 cases (2.3%) relapsed. Conclusion The onset age of CABM in children is usually within 1 year of age, especially <3 months. The primary pathogens in infants less than 3 months old are E. coli and GBS, and the dominant pathogen in children older than 3 months old is S. pneumoniae. Subdural effusion and (or) empyema and hydrocephalus are common complications. CABM should not be excluded even if CSF leukocyte counts are within normal range. Due to the low detection rate of pathogens in children with CABM, standardized CSF bacteriological examination should be paid more attention to increase the pathogen detection rate. Non‑culture CSF detection methods may facilitate pathogenic diagnosis.
Collapse
Affiliation(s)
- Caiyun Wang
- Department of Infectious Disease, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, Zhejiang, People’s Republic of China
| | - Hongmei Xu
- Department of Infectious Disease, Children’s Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Gang Liu
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, People’s Republic of China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
| | - Jing Liu
- Department of Infectious Disease, Hunan Children’s Hospital, Changsha, Hunan, People’s Republic of China
| | - Hui Yu
- Department of Infectious Disease, The Children’s Hospital of Fudan University, Shanghai, People’s Republic of China
| | - Biquan Chen
- Department of Infection, Anhui Province Children’s Hospital, Hefei, Anhui, People’s Republic of China
| | - Guo Zheng
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Min Shu
- Department of Pediatrics, West China Second University Hospital, Sichuan University/ West China Women’s and Children’s Hospital, Chengdu, Sichuang, People’s Republic of China
| | - Lijun Du
- Department of Neurology, Children’s Hospital of Shanxi, Taiyuan, Shanxi, People’s Republic of China
| | - Zhiwei Xu
- Pediatric Inpatient Ward, The 2nd Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
| | - Lisu Huang
- Department of Infectious Disease, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, Zhejiang, People’s Republic of China
- Department of Infectious Disease, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Haibo Li
- Outpatient Department of Pediatrics, The First Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
| | - Sainan Shu
- Department of Pediatric Infection and Gastroenterology, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China
| | - Yinghu Chen
- Department of Infectious Disease, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, Zhejiang, People’s Republic of China
| | - On behalf of The CPBMS Study Group
- Department of Infectious Disease, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Hangzhou, Zhejiang, People’s Republic of China
- Department of Infectious Disease, Children’s Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, People’s Republic of China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Department of Infectious Disease, Hunan Children’s Hospital, Changsha, Hunan, People’s Republic of China
- Department of Infectious Disease, The Children’s Hospital of Fudan University, Shanghai, People’s Republic of China
- Department of Infection, Anhui Province Children’s Hospital, Hefei, Anhui, People’s Republic of China
- Department of Neurology, Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
- Department of Pediatrics, West China Second University Hospital, Sichuan University/ West China Women’s and Children’s Hospital, Chengdu, Sichuang, People’s Republic of China
- Department of Neurology, Children’s Hospital of Shanxi, Taiyuan, Shanxi, People’s Republic of China
- Pediatric Inpatient Ward, The 2nd Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, People’s Republic of China
- Department of Infectious Disease, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- Outpatient Department of Pediatrics, The First Hospital of Jilin University, Changchun, Jilin, People’s Republic of China
- Department of Pediatric Infection and Gastroenterology, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China
| |
Collapse
|
4
|
Morsli M, Salipante F, Kerharo Q, Boudet A, Stephan R, Dunyach-Remy C, Zandotti C, Lavigne JP, Drancourt M. Dynamics of community-acquired meningitis syndrome outbreaks in southern France. Front Microbiol 2023; 13:1102130. [PMID: 36777029 PMCID: PMC9909019 DOI: 10.3389/fmicb.2022.1102130] [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: 11/18/2022] [Accepted: 12/30/2022] [Indexed: 01/27/2023] Open
Abstract
In southern France, cases of community-acquired meningitis syndrome (CAM) are typically clustered as outbreaks with determinants which remain unknown. This 61-month retrospective investigation in Nîmes and Marseille university hospital laboratories, yielded 2,209/20,779 (10.63%) documented CAM cases caused by 62 different micro-organisms, represented by seasonal viral etiologies (78.8%), including Enterovirus, Herpes Simplex Virus (HSV), and Varicella-Zoster Virus (VZV; 1,620/2,209 = 73.4%). Multi correspondence analysis revealed an association of infection with age and sex, with the risk of infection being relatively higher in young men, as confirmed by Fisher's exact test (p < 10-3). Bacterial meningitis accounted for 20% of cases, mostly caused by Streptococcus pneumoniae (27.4% of cases), Neisseria meningitidis (12.5%), and Haemophilus influenzae (9.5%) with bacteria/virus coinfection (0.9%), and only six cases of documented fungal meningitis. In total, 62.6% of cases, of which 88.7% were undocumented, arose from 10 outbreaks. 33.2% of undocumented cases were aged >60 years compared to 19.2% of documented cases (p < 0.001), and viral infection was more common in the summer (87.5%) compared to other seasons (72.3%; p < 0.001). Outbreaks most often started in Nîmes and moved eastward toward Marseille at a speed of ~9 km/day, and these dynamics significantly correlated with atmospheric temperature, especially during summer outbreaks. In particular, the incidence of Enterovirus-driven outbreaks correlated with temperature, revealing correlation coefficients of 0.64 in Nîmes and 0.72 in Marseille, and its occurrence in Marseille lagged that in Nîmes by 1-2 weeks. Tracing the dynamics of CAM outbreak during this retrospective investigation in southern France yielded a speed of displacement that correlated with the variation in temperature between both cities, and these results provide clues for the next occurrence of undocumented outbreaks.
Collapse
Affiliation(s)
- Madjid Morsli
- IHU Méditerranée Infection, Marseille, France,Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Florian Salipante
- Laboratoire de biostatistique, Épidémiologie Clinique, Santé Publique, Innovation et Méthodologie, CHU de Nîmes, Université de Montpellier, Nîmes, France
| | - Quentin Kerharo
- Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
| | - Agathe Boudet
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Robin Stephan
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Catherine Dunyach-Remy
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Christine Zandotti
- IHU Méditerranée Infection, Marseille, France,Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France,Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France,Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France,*Correspondence: Michel Drancourt, ✉
| |
Collapse
|
5
|
Jiang C, Xu Z, Li J, Zhang J, Xue X, Jiang J, Jiang G, Wang X, Peng Y, Chen T, Liu Z, Xie L, Gao H, Liu Y, Yang Y. Case report: Clinical and virological characteristics of aseptic meningitis caused by a recombinant echovirus 18 in an immunocompetent adult. Front Med (Lausanne) 2023; 9:1094347. [PMID: 36714132 PMCID: PMC9878155 DOI: 10.3389/fmed.2022.1094347] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/14/2022] [Indexed: 01/13/2023] Open
Abstract
Echovirus 18 has been recognized as an important causative pathogen of aseptic meningitis in young children worldwide, and echovirus 18-induced meningitis is rarely found in adults with immunocompetence. In this case study, we report the clinical and virological characteristics of aseptic meningitis caused by recombinant echovirus 18 in an adult with immunocompetence. A 31-year-old woman with immunocompetence was admitted to our hospital with fever, dizziness, severe headache, nausea, and vomiting for the past 1 day and was diagnosed with viral meningitis based on the clinical manifestations and laboratory results from cerebrospinal fluid (CSF). The patient received antiviral treatment with ribavirin and interferon as soon as the enterovirus infection was identified using qRT-PCR and was cured after 4 days. From the oropharyngeal swab and CSF samples, two echovirus 18 strains were isolated with a single nucleotide difference located at the 5' UTR. Phylogenetic analyses based on the VP1 gene showed that the two strains belonged to the subgenotype C2 and were clustered with sequences obtained from China after 2015, while the results from the 3D polymerase region showed that the two strains were closely related to the E30 strains. Bootscanning results using the 5' UTR to 2A region and the 2B to 3' UTR region showed that potential intertypic recombination had occurred in the 2B gene. Recombination analyses further confirmed that the two strains (echovirus 18) presented genome recombination with echovirus 30 in the nucleotide regions of the 2B gene. To the best of our knowledge, this is the first report of echovirus 18-induced meningitis in an adult with immunocompetence from mainland China, highlighting the need for close surveillance of echovirus 18 both in children and adults in the future.
Collapse
Affiliation(s)
- Chunmei Jiang
- Department of Infectious Disease, The People’s Hospital of Longhua, Shenzhen, China
| | - Zhixiang Xu
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Jin Li
- Shenzhen Polytechnic, Shenzhen, China
| | - Jiaqi Zhang
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Xingkui Xue
- Department of Infectious Disease, The People’s Hospital of Longhua, Shenzhen, China
| | - Jingxia Jiang
- Department of Infectious Disease, The People’s Hospital of Longhua, Shenzhen, China
| | - Guihua Jiang
- Department of Infectious Disease, The People’s Hospital of Longhua, Shenzhen, China
| | - Xisheng Wang
- Department of Infectious Disease, The People’s Hospital of Longhua, Shenzhen, China
| | - Yun Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Tian Chen
- Department of Infectious Disease, The People’s Hospital of Longhua, Shenzhen, China
| | - Zhenzhen Liu
- Department of Infectious Disease, The People’s Hospital of Longhua, Shenzhen, China
| | - Liu Xie
- Department of Infectious Disease, The People’s Hospital of Longhua, Shenzhen, China
| | - Haibin Gao
- Department of Infectious Disease, The People’s Hospital of Longhua, Shenzhen, China,Haibin Gao,
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China,Yingxia Liu,
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China,*Correspondence: Yang Yang,
| |
Collapse
|
6
|
Meng LN, Li G, Yuan HX, Feng XC, Liu F, Zhang SL. Utility of metagenomics next-generation sequencing in the diagnosis and treatment of severe infectious diseases in the intensive care unit. Technol Health Care 2023; 31:1887-1899. [PMID: 37302051 DOI: 10.3233/thc-220856] [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: 06/12/2023]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is a new method that combines high-throughput sequencing and bioinformatics analysis. However, it has not become as popular due to the limited testing equipment and high costs and lack of family awareness with not much relevant intensive care unit (ICU) research data. OBJECTIVE To explore the clinical use and value of metagenomics next-generation sequencing (mNGS) in patients with sepsis in the ICU. METHODS We conducted a retrospective analysis of 102 patients with sepsis admitted to the ICU of Peking University International Hospital from January 2018 to January 2022. Based on whether mNGS was performed, the identified patients were divided into the observation group (n= 51) and the control group (n= 51), respectively. Routine laboratory tests, including routine blood test, C-reactive protein, procalcitonin, and culture of suspicious lesion specimens were performed in both groups within 2 hours after admission to the ICU, while mNGS tests were performed in the observation group. Patients in both groups were routinely given initial anti-infective, anti-shock, and organ support treatment. Antibiotic regimens were optimized in a timely manner according to the etiological results. Relevant clinical data were collected. RESULTS The testing cycle of mNGS was shorter than that of the conventional culture (30.79 ± 4.01 h vs. 85.38 ± 9.94 h, P< 0.001), while the positive rate of mNGS was higher than that of the conventional culture (82.35% vs. 45.1%, P< 0.05), with obvious superiority in the detection of viruses and fungus. There were significant differences in the optimal time of antibiotics (48 h vs.100 h) and length of ICU stay (11 d vs. 16 d) between the observation group and control group (P< 0.01) respectively, with no difference in 28-day mortality (33.3% vs. 41.2%, P> 0.05). CONCLUSION mNGS is useful in the detection of sepsis-causing pathogens in the ICU with the advantages of short testing time and high positive rate. There was no difference in the 28-day outcome between the two groups, which may be related to other confounding factors such as small sample size. Additional studies with extended sample size are needed.
Collapse
|
7
|
Aetiologies and clinical presentation of central nervous system infections in Vietnamese patients: a prospective study. Sci Rep 2022; 12:18065. [PMID: 36302889 PMCID: PMC9613671 DOI: 10.1038/s41598-022-23007-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 10/21/2022] [Indexed: 01/24/2023] Open
Abstract
Knowledge of the clinical presentation of central nervous system (CNS) infections and the causative pathogens is crucial for appropriate diagnosis and rapid initiation of appropriate treatment to prevent severe neurological sequelae. The aim of this study is to understand the aetiology of CNS infections based on the clinical presentation of Vietnamese patients. A prospective hospital-based cohort study was conducted between May 2014 and May 2017. We screened 137 patients with clinically suspected CNS infection for fungal, bacterial and viral pathogens using their cerebrospinal fluid (CSF) and blood cultures. In addition, DNA or RNA extracted from CSF samples were subjected to nucleic acid testing (NAT) with a selective panel of bacterial, viral and fungal pathogens. At least one pathogen could be detected in 41% (n = 56) of the patients. The main pathogens causing CNS infections were Streptococcus suis (n = 16; 12%) and Neisseria meningitidis (n = 9; 7%), followed by Herpes simplex virus 1/2 (n = 4; 3%) and Klebsiella pneumoniae (n = 4; 3%). Other pathogens were only identified in a few cases. Patients with bacterial CNS infections were significantly older, had a worse outcome, a lower Glasgow Coma Scale (GCS), a higher rate of speech impairment and neck stiffness than patients with viral or tuberculous CNS infections. In northern Vietnam, adults are mostly affected by bacterial CNS infections, which have a severe clinical course and worse outcomes compared to viral or tuberculous CNS infections. Clinicians should be aware of the regional occurrence of pathogens to initiate rapid and appropriate diagnosis and treatment.
Collapse
|
8
|
Zhang S, Wu G, Shi Y, Liu T, Xu L, Dai Y, Chang W, Ma X. Understanding etiology of community-acquired central nervous system infections using metagenomic next-generation sequencing. Front Cell Infect Microbiol 2022; 12:979086. [PMID: 36225235 PMCID: PMC9549810 DOI: 10.3389/fcimb.2022.979086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundCommunity-acquired central nervous system infections (CA-CNS infections) have the characteristics of acute onset and rapid progression, and are associated with high levels of morbidity and mortality worldwide. However, there have been only limited studies on the etiology of this infections. Here, metagenomic next-generation sequencing (mNGS), a comprehensive diagnosis method, facilitated us to better understand the etiology of CA-CNS infections.MethodsWe conducted a single-center retrospective study between September 2018 and July 2021 in which 606 cerebrospinal fluid (CSF) samples were collected from suspected CNS infectious patients for mNGS testing, and all positive samples were included in this analysisResultsAfter the exclusion criteria, a total of 131 mNGS-positive samples were finally enrolled. Bacterial, viral, fungal, parasitic, specific pathogen and mixed infections were accounted for 32.82% (43/131), 13.74% (18/131), 0.76% (1/131), 2.29% (3/131) and 6.87% (9/131), respectively. A total of 41 different pathogens were identified, including 16 bacteria, 12 viruses, 10 fungi, and 1 parasite and 3 specific pathogens. The most frequent infecting pathogens are Epstein-Barr virus (n = 14), Herpes simplex virus 1 (n = 14), Mycobacterium tuberculosis (n = 13), Streptococcus pneumoniae (n = 13), and Cryptococcus neoformans (n = 8). Some difficult-to-diagnose pathogen infections were also detected by mNGS, such as Streptococcus suis, Pseudorabies virus, Bunyavirus, Orientia tsutsugamushi and Toxoplasma gondii.ConclusionIn this study, mNGS identified a wide variety of pathogens of CA-CNS infections and many of which could not be detected by conventional methods. Our data provide a better understanding of the etiology of CA-CNS infections and show that mNGS represents a comparative screening of CSF in an unbiased manner for a broad range of human pathogens.
Collapse
Affiliation(s)
- Shanshan Zhang
- Department of Medical Oncology, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Gang Wu
- Department of Clinical Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yuru Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ting Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Liangfei Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yuanyuan Dai
- Department of Clinical Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wenjiao Chang
- Department of Clinical Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaoling Ma
- Department of Clinical Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- *Correspondence: Xiaoling Ma,
| |
Collapse
|
9
|
Berklite L, Mitchell S, Wheeler SE. Large viral meningoencephalitis CSF serologic panel lacks utility in clinical decisions and outcomes. Clin Biochem 2022; 109-110:17-22. [PMID: 36075469 DOI: 10.1016/j.clinbiochem.2022.09.001] [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: 06/20/2022] [Revised: 08/13/2022] [Accepted: 09/01/2022] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Accurate diagnosis of viral meningoencephalitis (VMe) and identification of the etiologic agent has clinical importance and large serology panels are available to aid in the detection of several viral pathogens. However, such panels are often send-out testing, with prolonged time to results, thus impacting the actionability of test results. We hypothesized these panels may not contribute to patient care and lack clinical utility. METHODS A retrospective review of all VMe CSF serology panels ordered at one pediatric (n = 53; 2017-2019) and two adult (n = 200; 2019-2020) tertiary care hospitals was performed to assess test clinical utility. Panels included serology for: Adenovirus, coxsackie and echoviruses, influenza, measles, lymphocytic choriomeningitis virus, herpes simplex virus, mumps, varicella zoster, encephalitis viruses. Clinical data collected included diagnostic test results, symptoms, comorbidities, and interventions. RESULTS In 129/200 (64.5 %) of adult cases and 37/53 (69.8 %) of pediatric cases CSF had a WBC less than 5 cells/mm2. In total, 127 (63.5 %, 127/200) adult panels had at least one positive target with 49 panels having more than one positive (38.6 %, 49/127). In 99.5 % of adult and 100 % of pediatric cases there was no change to decisions regarding starting, discontinuing, continuing, or changing antimicrobial therapy based on panel results. In no cases were potentially immunosuppressive therapies like steroid or IVIG administration delayed while awaiting the results of the panel. CONCLUSIONS While all patients presented with neurologic symptoms, poor pre-screening for CNS inflammation using CSF WBC analysis likely contributed to poor clinical utility of the VMe panels. Large CSF serologic panels for VMe did not contribute to or add value to clinical decision making in our cohort.
Collapse
Affiliation(s)
- Lara Berklite
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Stephanie Mitchell
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah E Wheeler
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
10
|
Chen W, Wu Y, Zhang Y. Next-Generation Sequencing Technology Combined With Multiplex Polymerase Chain Reaction as a Powerful Detection and Semiquantitative Method for Herpes Simplex Virus Type 1 in Adult Encephalitis: A Case Report. Front Med (Lausanne) 2022; 9:905350. [PMID: 35783632 PMCID: PMC9240313 DOI: 10.3389/fmed.2022.905350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/23/2022] [Indexed: 11/25/2022] Open
Abstract
Background Traditional testing for specific microbes or categories of central nervous system (CNS) infectious diseases is often limited in sensitivity and timeliness. However, failure to initiate a timely etiological diagnosis and corresponding treatment in patients with neurologic infections contribute to poor outcomes. Case Summary A 58 year-old male presented acutely with fever, abnormal mental behavior, seizures and decreased consciousness. Brain magnetic resonance imaging (MRI) showed an abnormal FLAIR/T2 signal mainly in the left thalamus, temporal lobe, insular lobe, and bilateral hippocampus. To identify the pathogen, the cerebrospinal fluid (CSF) sample of the patient was used for metagenomic next-generation sequencing (mNGS) analysis and multiplex polymerase chain reaction (mPCR). The results showed 188 herpes simplex virus (HSV-1)-specific sequences. After acyclovir and foscarnet sodium treatment, the ratio of HSV-1/internal reference reads decreased from 813/493 to 695/1961, which coincided with clinical remission. Conclusion This study indicates that mNGS combined with mPCR may be an effective method for etiological diagnostic and dynamic clinical surveillance for HSV-1 encephalitis.
Collapse
|
11
|
Abstract
Neonatal bacterial meningitis is a devastating disease, associated with high mortality and neurological disability, in both developed and developing countries. Streptococcus agalactiae, commonly referred to as group B Streptococcus (GBS), remains the most common bacterial cause of meningitis among infants younger than 90 days. Maternal colonization with GBS in the gastrointestinal and/or genitourinary tracts is the primary risk factor for neonatal invasive disease. Despite prophylactic intrapartum antibiotic administration to colonized women and improved neonatal intensive care, the incidence and morbidity associated with GBS meningitis have not declined since the 1970s. Among meningitis survivors, a significant number suffer from complex neurological or neuropsychiatric sequelae, implying that the pathophysiology and pathogenic mechanisms leading to brain injury and devastating outcomes are not yet fully understood. It is imperative to develop new therapeutic and neuroprotective approaches aiming at protecting the developing brain. In this review, we provide updated clinical information regarding the understanding of neonatal GBS meningitis, including epidemiology, diagnosis, management, and human evidence of the disease's underlying mechanisms. Finally, we explore the experimental models used to study GBS meningitis and discuss their clinical and physiologic relevance to the complexities of human disease.
Collapse
|
12
|
Trujillo-Gómez J, Tsokani S, Arango-Ferreira C, Atehortúa-Muñoz S, Jimenez-Villegas MJ, Serrano-Tabares C, Veroniki AA, Florez ID. Biofire FilmArray Meningitis/Encephalitis panel for the aetiological diagnosis of central nervous system infections: A systematic review and diagnostic test accuracy meta-analysis. EClinicalMedicine 2022; 44:101275. [PMID: 35198914 PMCID: PMC8851290 DOI: 10.1016/j.eclinm.2022.101275] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/30/2021] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The FilmArray Meningitis/Encephalitis(FA/ME) panel brings benefits in clinical practice, but its diagnostic test accuracy (DTA) remains unclear. We aimed to determine the DTA of FA/ME for the aetiological diagnostic in patients with suspected central nervous system(CNS) infection. METHODS We performed a systematic review with DTA meta-analysis (PROSPERO: CRD42020139285). We searched Embase, Medline (Ovid), and Web of Science from inception until September 1st, 2021. We assessed the study-level risk of bias with the QUADAS-2 tool and applied the GRADE approach to assess the certainty of the synthesised evidence. We included studies that simultaneously measured the reference test (CSF/blood culture for bacteria, and specific polymerase chain reaction for viruses) and the FA/ME in patients with suspected CNS infection. We performed random-effects bivariate meta-analysis models of combined sensitivity and specificity using CSF/blood cultures(reference test 1) and a final diagnosis adjudication based on clinical/laboratory criteria (reference test 2). FINDINGS We included 19 studies (11,351 participants). For all bacteria with reference test 1 (16 studies/6183 patients) sensitivity was estimated at 89·5% (95%CI 81·1-94·4), and specificity at 97·4% (95%CI 94-98·9). With reference test 2 (15 studies/5,524 patients), sensitivity was estimated at 92·1%(95%CI 86·8-95·3) and specificity at 99.2(95%CI 98·3-99·6) For herpes simplex virus-2(HSV-2), enteroviruses, and Varicella-Zoster virus (VZV), we obtained sensitivities between 75·5 and 93·8%, and specificities above 99% (reference test 1). Certainty of the evidence was low. INTERPRETATION FA/ME may have acceptable-to-high sensitivities and high specificities for identifying bacteria, especially for S.pneumoniae, and viruses, especially for HSV-2, and enteroviruses. Sensitivities for L.monocytogenes, H.influenzae, E.coli, and HSV-1 were suboptimal. FUNDING None.
Collapse
Affiliation(s)
- Juliana Trujillo-Gómez
- Department of Paediatrics, Universidad de Antioquia, Calle 67 No. 53-108, Medellín, Antioquia 050001, Colombia
- Hospital San Vicente Fundacion, Calle 64 # 51D - 154, Medellín 050010, Colombia
- Hospital General de Medellín, Carrera 48 # 32-102, Medellín 0500515, Colombia
| | - Sofia Tsokani
- Department of Primary Education, School of Education, University of Ioannina, PO Box: 1186, Ioannina 45110, Greece
| | - Catalina Arango-Ferreira
- Department of Paediatrics, Universidad de Antioquia, Calle 67 No. 53-108, Medellín, Antioquia 050001, Colombia
- Hospital San Vicente Fundacion, Calle 64 # 51D - 154, Medellín 050010, Colombia
| | | | - Maria José Jimenez-Villegas
- Department of Paediatrics, Universidad de Antioquia, Calle 67 No. 53-108, Medellín, Antioquia 050001, Colombia
- Hospital San Vicente Fundacion, Calle 64 # 51D - 154, Medellín 050010, Colombia
| | - Carolina Serrano-Tabares
- Department of Paediatrics, Universidad de Antioquia, Calle 67 No. 53-108, Medellín, Antioquia 050001, Colombia
- Clínica Universitaria Bolivariana, Carrera 72A # 78b -50, Medellín 050015, Colombia
| | - Areti-Angeliki Veroniki
- St. Michael's Hospital, Li Ka Shing Knowledge Institute, 8 Shuter St, Toronto, ON M5B 1A6, Canada
| | - Ivan D. Florez
- Department of Paediatrics, Universidad de Antioquia, Calle 67 No. 53-108, Medellín, Antioquia 050001, Colombia
- School of Rehabilitation Science, McMaster University, 1400 Main St. W. Hamilton, Hamilton, ON L8S 1C7, Canada
- Paediatric Intensive Care Unit, Clínica Las Americas AUNA, Dg. 75B ##2A-80/140, Medellin, Colombia
- Corresponding author at: Department of Paediatrics, Universidad de Antioquia, Calle 67 No. 53-108, Medellín, Antioquia 050001, Colombia.
| |
Collapse
|
13
|
Xu G, Liu S, Li X, Quan X, Deng H, Liu L, Zheng X, Li X, Liu L. A case of meningoencephalocele in the nasal cavity 6 years after skull base fracture. Neurol Sci 2021; 42:5379-5384. [PMID: 34557967 DOI: 10.1007/s10072-021-05604-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/10/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Guanghui Xu
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Xianglin Road, Luzhou, 646000, Sichuan, China
| | - Shengjie Liu
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Xianglin Road, Luzhou, 646000, Sichuan, China
| | - Xin Li
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Xianglin Road, Luzhou, 646000, Sichuan, China
| | - Xingyun Quan
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Xianglin Road, Luzhou, 646000, Sichuan, China
| | - Huajiang Deng
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Xianglin Road, Luzhou, 646000, Sichuan, China
| | - Luotong Liu
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Xianglin Road, Luzhou, 646000, Sichuan, China
| | - Xiaomei Zheng
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Xianglin Road, Luzhou, 646000, Sichuan, China
| | - Xianglong Li
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Xianglin Road, Luzhou, 646000, Sichuan, China
| | - Liang Liu
- Department of Neurosurgery, Affiliated Hospital of Southwest Medical University, Xianglin Road, Luzhou, 646000, Sichuan, China. .,Sichuan Clinical Research Center for Neurosurgery, Luzhou, Sichuan, China. .,Academician (Expert) Workstation of Sichuan Province, Luzhou, Sichuan, China. .,Neurological Diseases and Brain Function Laboratory, Luzhou, Sichuan, China.
| |
Collapse
|
14
|
Hansen MA, Samannodi MS, Castelblanco RL, Hasbun R. Reply to Mathon et al. Clin Infect Dis 2021; 72:e433. [PMID: 32756937 DOI: 10.1093/cid/ciaa1094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael A Hansen
- Department of Family and Community Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Mohammed S Samannodi
- Department of Internal Medicine, UT Health McGovern Medical School, Houston, Texas, USA
| | | | - Rodrigo Hasbun
- Department of Internal Medicine, UT Health McGovern Medical School, Houston, Texas, USA
| |
Collapse
|
15
|
Geteneh A, Kassa T, Alemu D, Kiros M, Andualem H, Tenna A, Tesfaye A, Alemayehu DH, Mihret A, Howe R, Mulu A, Mihret W. Viral Etiologies of Meningitis in Patients with Presumed Pyogenic Meningitis at University Hospitals in Ethiopia. Infect Drug Resist 2021; 14:1083-1088. [PMID: 33762832 PMCID: PMC7982549 DOI: 10.2147/idr.s304521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/05/2021] [Indexed: 01/09/2023] Open
Abstract
Introduction Viral meningitis is common in most resource-limited settings, posing a challenge for the management and prognosis of suspected patients. No study has been done on the detection of either viral or viral-bacterial co-infection among presumed pyogenic meningitis cases in Ethiopia. We, therefore, aimed to determine the distribution of cytomegalovirus (CMV) and human enteroviruses (HEVs) among patients with presumptive pyogenic meningitis at University hospitals in Ethiopia. Methods Viral nucleic acid was extracted from 86 repository CSF samples, which were collected from patients presumptively diagnosed with pyogenic meningitis between 2012 and 2013. PCR was done consecutively to investigate the possible viral etiologic agents of meningitis. Results HEVs were detected in 11 (12.8%) of the analyzed samples while none of the 86 samples were tested positive for CMV. Viral-bacterial co-infections were found among 4/11 (36.4%) confirmed cases. The majority of the patients (10/11) with HEVs were younger aged ≤ 19 years old. Conclusions In this study, the magnitude of HEVs was shown to have a significant role in presumed pyogenic meningitis cases. Therefore, we recommend presumed pyogenic meningitis cases to be inspected for viral etiologies and improve meningeal symptoms interpretations.
Collapse
Affiliation(s)
- Alene Geteneh
- Department of Medical Laboratory Science, College of Health Science, Woldia University, Woldia, Ethiopia
| | - Tesfaye Kassa
- School of Medical Laboratory Science, Jimma University, Jimma, Ethiopia
| | - Derbie Alemu
- Department of Medical Laboratory Science, Arba Minch College of Health Science, Arba Minch, Ethiopia
| | - Mulugeta Kiros
- Department of Medical Laboratory Science, College of Health Science, Debre Tabor University, Debre Tabor, Ethiopia
| | - Henok Andualem
- Department of Medical Laboratory Science, College of Health Science, Debre Tabor University, Debre Tabor, Ethiopia
| | - Admasu Tenna
- School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Rawleigh Howe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Wude Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| |
Collapse
|
16
|
Tsamis KI, Sakkas H, Giannakis A, Ryu HS, Gartzonika C, Nikas IP. Evaluating Infectious, Neoplastic, Immunological, and Degenerative Diseases of the Central Nervous System with Cerebrospinal Fluid-Based Next-Generation Sequencing. Mol Diagn Ther 2021; 25:207-229. [PMID: 33646562 PMCID: PMC7917176 DOI: 10.1007/s40291-021-00513-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 12/24/2022]
Abstract
Cerebrospinal fluid (CSF) is a clear and paucicellular fluid that circulates within the ventricular system and the subarachnoid space of the central nervous system (CNS), and diverse CNS disorders can impact its composition, volume, and flow. As conventional CSF testing suffers from suboptimal sensitivity, this review aimed to evaluate the role of next-generation sequencing (NGS) in the work-up of infectious, neoplastic, neuroimmunological, and neurodegenerative CNS diseases. Metagenomic NGS showed improved sensitivity—compared to traditional methods—to detect bacterial, viral, parasitic, and fungal infections, while the overall performance was maximized in some studies when all diagnostic modalities were used. In patients with primary CNS cancer, NGS findings in the CSF were largely concordant with the molecular signatures derived from tissue-based molecular analysis; of interest, additional mutations were identified in the CSF in some glioma studies, reflecting intratumoral heterogeneity. In patients with metastasis to the CNS, NGS facilitated diagnosis, prognosis, therapeutic management, and monitoring, exhibiting higher sensitivity than neuroimaging, cytology, and plasma-based molecular analysis. Although evidence is still rudimentary, NGS could enhance the diagnosis and pathogenetic understanding of multiple sclerosis in addition to Alzheimer and Parkinson disease. To conclude, NGS has shown potential to aid the research, facilitate the diagnostic approach, and improve the management outcomes of all the aforementioned CNS diseases. However, to establish its role in clinical practice, the clinical validity and utility of each NGS protocol should be determined. Lastly, as most evidence has been derived from small and retrospective studies, results from randomized control trials could be of significant value.
Collapse
Affiliation(s)
- Konstantinos I Tsamis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece. .,School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus.
| | - Hercules Sakkas
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Alexandros Giannakis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, 03080, Korea
| | - Constantina Gartzonika
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Ilias P Nikas
- School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus
| |
Collapse
|
17
|
Perlejewski K, Bukowska-Ośko I, Rydzanicz M, Pawełczyk A, Caraballo Cortѐs K, Osuch S, Paciorek M, Dzieciątkowski T, Radkowski M, Laskus T. Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations. Sci Rep 2020; 10:16173. [PMID: 32999423 PMCID: PMC7528011 DOI: 10.1038/s41598-020-73156-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022] Open
Abstract
Identification of pathogens causing viral encephalitis remains challenging, and in over 50% of cases the etiologic factor remains undetermined. Next-generation sequencing (NGS) based metagenomics has been successfully used to detect novel and rare infections, but its value for routine diagnosis of encephalitis remains unclear. The aim of the present study was to determine the sensitivity of shotgun metagenomic sequencing protocols, which include preamplification, and testing it against cerebrospinal fluid (CSF) samples from encephalitis patients. For sensitivity testing HIV and HBV positive sera were serially diluted in CSF from an uninfected patient. NGS repeatedly detected HIV and HBV sequences present at concentrations from 105 to 102 and from 105 to 10 viral copies/reaction, respectively. However, when the same protocols were applied to RT-PCR/PCR positive CSF samples from 6 patients with enteroviral encephalitis (median viral load 47 copies/ml) and 15 patients with HSV, CMV or VZV encephalitis (median viral load 148 copies/ml), only 7 (28.6%) were identified as positive. In conclusions, while NGS has the advantage of being able to identify a wide range of potential pathogens it seems to be less sensitive compared to the standard amplification-based assays in the diagnosis of encephalitis, where low viral loads are common.
Collapse
Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland.
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortѐs
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Sylwia Osuch
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Paciorek
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | | | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| |
Collapse
|
18
|
Farraj SA, El-Kafrawy SA, Kumosani TA, Yousef JM, Azhar EI. Evaluation of Extraction Methods for Clinical Metagenomic Assay. Microorganisms 2020; 8:microorganisms8081128. [PMID: 32727010 PMCID: PMC7465710 DOI: 10.3390/microorganisms8081128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 02/02/2023] Open
Abstract
(1) Background: Clinical metagenomics is a promising approach that helps to identify etiological agents in cases of unknown infections. For the efficient detection of an unknown pathogen, the extraction method must be carefully selected for the maximum recovery of nucleic acid from different microorganisms. The aim of this study was to evaluate different extraction methods that have the ability to isolate nucleic acids from different types of pathogens with good quality and quantity for efficient use in clinical metagenomic identification. (2) Methods: A mock sample spiked with five different pathogens was used for the comparative evaluation of different commercial extraction kits. Extracted samples were subjected to library preparation and run on MiSeq. The selected extraction method based on the outcome of the comparative evaluation was used subsequently for the nucleic acid isolation of all infectious agents in clinical respiratory samples with multiple infections. (3) Results: The protocol using the PowerViral® Environmental RNA-DNA Isolation Kit with a 5-min bead beating step achieved the best results with a low starting volume. The analysis of the tested clinical specimens showed the ability to successfully identify different types of pathogens. (4) Conclusions: The optimized extraction protocol in this study is recommended for clinical metagenomics application in specimens with multiple infections from different taxa.
Collapse
Affiliation(s)
- Suha A. Farraj
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.F.); (T.A.K.); (J.M.Y.)
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Shreif A. El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Clinical Pathology Department, National Liver Institute, Menoufia University, Shebin El-Kom 32511, Egypt
- Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Taha A. Kumosani
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.F.); (T.A.K.); (J.M.Y.)
- Central Laboratory for Food and Nutrition, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jehad M. Yousef
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.F.); (T.A.K.); (J.M.Y.)
- Department of Biochemistry, College of Sciences, University of Jeddah, Jeddah 23890, Saudi Arabia
| | - Esam I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence:
| |
Collapse
|
19
|
Hasan MR, Sundararaju S, Tang P, Tsui KM, Lopez AP, Janahi M, Tan R, Tilley P. A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting. Sci Rep 2020; 10:11194. [PMID: 32641704 PMCID: PMC7343800 DOI: 10.1038/s41598-020-68159-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/16/2020] [Indexed: 01/22/2023] Open
Abstract
The etiology of central nervous system (CNS) infections such as meningitis and encephalitis remains unknown in a large proportion of cases partly because the diversity of pathogens that may cause CNS infections greatly outnumber available test methods. We developed a metagenomic next generation sequencing (mNGS)-based approach for broad-range detection of pathogens associated with CNS infections suitable for application in the acute care hospital setting. The analytical sensitivity of mNGS performed on an Illumina MiSeq was assessed using simulated cerebrospinal fluid (CSF) specimens (n = 9). mNGS data were then used as a training dataset to optimize a bioinformatics workflow based on the IDseq pipeline. For clinical validation, residual CSF specimens (n = 74) from patients with suspected CNS infections previously tested by culture and/or PCR, were analyzed by mNGS. In simulated specimens, the NGS reads aligned to pathogen genomes in IDseq were correlated to qPCR CT values for the respective pathogens (R = 0.96; p < 0.0001), and the results were highly specific for the spiked pathogens. In clinical samples, the diagnostic accuracy, sensitivity and specificity of the mNGS with reference to conventional methods were 100%, 95% and 96%, respectively. The clinical application of mNGS holds promise to benefit patients with CNS infections of unknown etiology.
Collapse
Affiliation(s)
- Mohammad Rubayet Hasan
- Department of Pathology, Sidra Medicine, Level 2M, Office H2M-24093, PO BOX 26999, Doha, Qatar. .,Weill Cornell Medical College in Qatar, Doha, Qatar. .,Sidra Medicine, Doha, Qatar.
| | | | - Patrick Tang
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Kin-Ming Tsui
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Andres Perez Lopez
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Mohammad Janahi
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Rusung Tan
- Weill Cornell Medical College in Qatar, Doha, Qatar.,Sidra Medicine, Doha, Qatar
| | - Peter Tilley
- British Columbia Children's Hospital, Vancouver, BC, Canada.,University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
20
|
Implementation of the eazyplex® CSF direct panel assay for rapid laboratory diagnosis of bacterial meningitis: 32-month experience at a tertiary care university hospital. Eur J Clin Microbiol Infect Dis 2020; 39:1845-1853. [DOI: 10.1007/s10096-020-03909-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022]
|
21
|
Evans M, Merkel KG, Harder J, Rose DT. Impact of the implementation of a rapid meningitis/encephalitis multiplex polymerase chain reaction panel on IV acyclovir duration: multicenter, retrospective cohort of adult and pediatric patients. Diagn Microbiol Infect Dis 2020; 96:114935. [DOI: 10.1016/j.diagmicrobio.2019.114935] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 11/03/2019] [Accepted: 11/03/2019] [Indexed: 11/30/2022]
|
22
|
Säll O, Thulin Hedberg S, Neander M, Tiwari S, Dornon L, Bom R, Lagerqvist N, Sundqvist M, Mölling P. Etiology of Central Nervous System Infections in a Rural Area of Nepal Using Molecular Approaches. Am J Trop Med Hyg 2020; 101:253-259. [PMID: 31162021 PMCID: PMC6609203 DOI: 10.4269/ajtmh.18-0434] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The etiology of infections of the central nervous system (CNS) in Nepal often remains unrecognized because of underdeveloped laboratory facilities. The aim of this study was to investigate the etiology of CNS infections in a rural area of Nepal using molecular methods. From November 2014 to February 2016, cerebrospinal fluid (CSF) was collected from 176 consecutive patients presenting at United Mission Hospital in Tansen, Nepal, with symptoms of possible CNS infection. After the CSF samples were stored and transported frozen, polymerase chain reaction (PCR) was performed in Sweden, targeting a total of 26 pathogens using the FilmArray® ME panel (BioFire, bioMerieux, Salt Lake City, UT), the MeningoFinder® 2SMART (PathoFinder, Maastricht, The Netherlands), and an in-house PCR test for dengue virus (DENV), Japanese encephalitis virus (JEV), and Nipah virus (NiV). The etiology could be determined in 23%. The bacteria detected were Haemophilus influenzae (n = 5), Streptococcus pneumoniae (n = 4), and Neisseria meningitidis (n = 1). The most common virus was enterovirus detected in eight samples, all during the monsoon season. Other viruses detected were cytomegalovirus (n = 6), varicella zoster virus (n = 5), Epstein–Barr virus (n = 3), herpes simplex virus (HSV) type 1 (HSV-1) (n = 3), HSV-2 (n = 3), human herpes virus (HHV) type 6 (HHV-6) (n = 3), and HHV-7 (n = 2). Cryptococcus neoformans/gatti was found in four samples. None of the samples were positive for DENV, JEV, or NiV. Of the patients, 67% had been exposed to antibiotics before lumbar puncture. In conclusion, the etiology could not be found in 77% of the samples, indicating that the commercial PCR panels used are not suitable in this setting. Future studies on the etiology of CNS infections in Nepal could include metagenomic techniques.
Collapse
Affiliation(s)
- Olof Säll
- Department of Infectious Diseases, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Sara Thulin Hedberg
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Marita Neander
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | | | - Rabin Bom
- United Mission Hospital Tansen, Tansen, Nepal
| | | | - Martin Sundqvist
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Paula Mölling
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| |
Collapse
|
23
|
Domínguez-Gil M, Artero A, Oteo JA, Eiros JM. Virología: diagnóstico sindrómico de meningitis y encefalitis. Enferm Infecc Microbiol Clin 2020; 38 Suppl 1:19-23. [DOI: 10.1016/j.eimc.2020.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
24
|
Au CC, Hon KL, Leung AKC, Torres AR. Childhood Infectious Encephalitis: An Overview of Clinical Features, Investigations, Treatment, and Recent Patents. RECENT PATENTS ON INFLAMMATION & ALLERGY DRUG DISCOVERY 2020; 14:156-165. [PMID: 33238854 DOI: 10.2174/1872213x14999201124195724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Infectious encephalitis is a serious and challenging condition to manage. This overview summarizes the current literature regarding the etiology, clinical manifestations, diagnosis, management, and recent patents of acute childhood infectious encephalitis. METHODS We used PubMed Clinical Queries as a search engine and used keywords of "encephalitis" AND "childhood" Patents were searched using the key term "encephalitis" in google.patents.- com and patentsonline.com. RESULTS Viral encephalitis is the most common cause of acute infectious encephalitis in children. In young children, the clinical manifestations can be non-specific. Provision of empiric antimicrobial therapy until a specific infectious organism has been identified, which in most cases includes acyclovir, is the cornerstone of therapy. Advanced investigation tools, including nucleic acid-based test panel and metagenomic next-generation sequencing, improve the diagnostic yield of identifying an infectious organism. Supportive therapy includes adequate airway and oxygenation, fluid and electrolyte balance, cerebral perfusion pressure support, and seizure control. Recent patents are related to the diagnosis, treatment, and prevention of acute infectious encephalitis. CONCLUSION Viral encephalitis is the most common cause of acute infectious encephalitis in children and is associated with significant morbidity. Recent advances in understanding the genetic basis and immunological correlation of infectious encephalitis may improve treatment. Third-tier diagnostic tests may be incorporated into clinical practice. Treatment is targeted at the infectious process but remains mostly supportive. However, specific antimicrobial agents and vaccines development is ongoing.
Collapse
Affiliation(s)
- Cheuk C Au
- Department of Paediatrics and Adolescent Medicine, The Hong Kong Children's Hospital, Kowloon Bay, Kowloon, Hong Kong
| | - Kam L Hon
- Department of Paediatrics and Adolescent Medicine, The Hong Kong Children's Hospital, Kowloon Bay, Kowloon, Hong Kong
| | - Alexander K C Leung
- Department of Pediatrics, The University of Calgary and The Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Alcy R Torres
- Department of Pediatrics, Division of Pediatric Neurology, Pediatric Traumatic Brain Injury Program, Associate Professor of Pediatrics and Neurology, Boston University, School of Medicine, Boston, MA, United States
| |
Collapse
|
25
|
Abstract
The role of biomarkers for detection of sepsis has come a long way. Molecular biomarkers are taking front stage at present, but machine learning and other computational measures using bigdata sets are promising. Clinical research in sepsis is hampered by lack of specificity of the diagnosis; sepsis is a syndrome with no uniformly agreed definition. This lack of diagnostic precision means there is no gold standard for this diagnosis. The final conclusion is expert opinion, which is not bad but not perfect. Perhaps machine learning will displace expert opinion as the final and most accurate definition for sepsis.
Collapse
Affiliation(s)
- Steven M Opal
- Infectious Disease Division, Alpert Medical School of Brown University, Ocean State Clinical Coordinating Center at Rhode Island Hospital, 1 Virginia Avenue Suite 105, Providence, RI 02905, USA.
| | - Xavier Wittebole
- Critical Care Department, (Pr Laterre), Cliniques Universitaires Saint-Luc, Avenue Hippocrate 10, 1200 Brussels, Belgium
| |
Collapse
|
26
|
Du B, Hua C, Xia Y, Li J, Xie Y, Tao Y, Cao Q, Mo X. Evaluation of the BioFire FilmArray meningitis/encephalitis panel for the detection of bacteria and yeast in Chinese children. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:437. [PMID: 31700873 DOI: 10.21037/atm.2019.08.103] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Background Meningitis and encephalitis are life-threatening syndromes with high morbidity and mortality in children. Due to limitations of traditional laboratory approaches in etiological diagnosis, the rate of misdiagnoses is unacceptably high. Methods We retrospectively compared the potential clinical impact of the FilmArray meningitis/encephalitis (ME) panel vs. conventional cerebrospinal fluid (CSF) culture in children with central nervous system (CNS) infections. Sixty-eight pediatric patients (<18 years of age) with an initial diagnosis of meningitis or encephalitis were enrolled at 2 children's hospital from January to October 2017. Results Fifteen specimens were found to be positive after CSF culture, with a positive rate of 22.1% (15/68). For the FilmArray ME panel, 26 bacteria and fungi from 25 samples were detected, and the positive rate was 36.8% (25/68). The FilmArray ME panel identified 14 pathogens in previously pathogen-negative patients. Conclusions This study demonstrated the capability of the FilmArray ME panel in the diagnosis of bacterial and fungal meningitis and therefore its potential use in facilitating enhanced patient care.
Collapse
Affiliation(s)
- Bailu Du
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Chunzhen Hua
- Department of Infectious Diseases, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Yijun Xia
- Department of Medical Affairs, bioMérieux (Shanghai) Company Limited, Shanghai 201315, China
| | - Jin Li
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yongping Xie
- Department of Infectious Diseases, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Yue Tao
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Qing Cao
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xi Mo
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| |
Collapse
|
27
|
Beganovic M, McCreary EK, Mahoney MV, Dionne B, Green DA, Timbrook TT. Interplay between Rapid Diagnostic Tests and Antimicrobial Stewardship Programs among Patients with Bloodstream and Other Severe Infections. J Appl Lab Med 2018; 3:601-616. [PMID: 31639729 DOI: 10.1373/jalm.2018.026450] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Antimicrobial stewardship programs (ASPs) aim to provide optimal antimicrobial therapy to patients quickly to improve the likelihood of overcoming infection while reducing the risk of adverse effects. Rapid diagnostic tests (RDTs) for infectious diseases have become an integral tool for ASPs to achieve these aims. CONTENT This review explored the demonstrated clinical value of longer-standing technologies and implications of newer RDTs from an antimicrobial stewardship perspective. Based on available literature, the focus was on the use of RDTs in bloodstream infections (BSIs), particularly those that perform organism identification and genotypic resistance detection, phenotypic susceptibility testing, and direct specimen testing. Clinical implications of rapid testing among respiratory, central nervous system, and gastrointestinal infections are also reviewed. SUMMARY Coupling RDTs with ASPs facilitates the appropriate and timely use of test results, translating into improved patient outcomes through optimization of antimicrobial use. These benefits are best demonstrated in the use of RDT in BSIs. Rapid phenotypic susceptibility testing offers the potential for early pharmacokinetic/pharmacodynamic optimization, and direct specimen testing on blood may allow ASPs to initiate appropriate therapy and/or tailor empiric therapy even sooner than other RDTs. RDTs for respiratory, central nervous system, and gastrointestinal illnesses have also shown significant promise, although more outcome studies are needed to evaluate their full impact.
Collapse
Affiliation(s)
- Maya Beganovic
- Advocate Lutheran General Hospital, Department of Pharmacy, Park Ridge, IL
| | - Erin K McCreary
- University of Pittsburgh Medical Center, Department of Pharmacy, Pittsburgh, PA
| | - Monica V Mahoney
- Beth Israel Deaconess Medical Center, Department of Pharmacy, Boston, MA
| | - Brandon Dionne
- Northeastern University, School of Pharmacy, Bouvé College of Health Sciences, Boston, MA.,Brigham and Women's Hospital, Department of Pharmacy, Boston, MA
| | - Daniel A Green
- Columbia University College of Physicians and Surgeons, New York, NY
| | | |
Collapse
|
28
|
Diagnostic Approach to Health Care- and Device-Associated Central Nervous System Infections. J Clin Microbiol 2018; 56:JCM.00861-18. [PMID: 30135235 DOI: 10.1128/jcm.00861-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Health care- and device-associated central nervous system (CNS) infections have a distinct epidemiology, pathophysiology, and microbiology that require a unique diagnostic approach. Most clinical signs, symptoms, and tests used to diagnose community-acquired CNS infections are insensitive and nonspecific in neurosurgical patients due to postsurgical changes, invasive devices, prior antimicrobial exposure, and underlying CNS disease. The lack of a standardized definition of infection or diagnostic pathway has added to this challenge. In this review, we summarize the epidemiology, microbiology, and clinical presentation of these infections, discuss the issues with existing microbiologic tests, and give an overview of the current diagnostic approach.
Collapse
|
29
|
|
30
|
Pérez-Ruiz M, Pedrosa-Corral I, Sanbonmatsu-Gámez S, Gómez-Camarasa C, Navarro-Marí JM. Analytical validation of viral CNS Flow Chip kit for detection of acute meningitis and encephalitis. J Virol Methods 2018; 259:54-59. [PMID: 29902492 DOI: 10.1016/j.jviromet.2018.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/17/2018] [Accepted: 06/10/2018] [Indexed: 01/14/2023]
Abstract
A new molecular assay (Viral CNS Flow Chip kit, Master Diagnóstica, Spain) has been developed for the detection of eight viruses causing acute meningitis and encephalitis, i.e. herpes simplex viruses 1-2, varicella zoster virus, human enterovirus, human parechovirus, Toscana virus, human cytomegalovirus and Epstein Barr virus. The new assay is a multiplex one-step RT-PCR followed by automatic flow-through hybridization, colorimetric detection and image analysis. The limit of detection was 50 copies/reaction, and 10 copies/reaction for human enterovirus and the other seven viruses, respectively. The analytical validation was performed with nucleic acids extracted from 268 cerebrospinal fluid samples and the results were compared with routine molecular assays. An excellent coefficient of agreement was observed between V-CNS and routine assays [kappa index: 0.948 (95%CI: 0.928-0.968)]. The overall sensitivity and specificity was 95.9% (95%CI: 91.2-98.3%) and 99.9% (95%CI: 99.6-100%), respectively. Viral CNS Flow Chip kit is an efficient multiplex platform for the detection of the main viruses involved in acute meningitis and encephalitis. The inclusion of a TOSV genome target may improve the laboratory diagnosis of viral neurological infections in endemic areas.
Collapse
Affiliation(s)
- Mercedes Pérez-Ruiz
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Avda. Fuerzas Armadas, 2, Granada, 18014, Spain.
| | - Irene Pedrosa-Corral
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Avda. Fuerzas Armadas, 2, Granada, 18014, Spain
| | - Sara Sanbonmatsu-Gámez
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Avda. Fuerzas Armadas, 2, Granada, 18014, Spain
| | - Cristina Gómez-Camarasa
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Avda. Fuerzas Armadas, 2, Granada, 18014, Spain
| | - José María Navarro-Marí
- Servicio de Microbiología, Hospital Universitario Virgen de las Nieves, Instituto de Investigación Biosanitaria de Granada, Avda. Fuerzas Armadas, 2, Granada, 18014, Spain
| |
Collapse
|
31
|
One Year in the Life of a Rapid Syndromic Panel for Meningitis/Encephalitis: a Pediatric Tertiary Care Facility's Experience. J Clin Microbiol 2018. [PMID: 29540454 DOI: 10.1128/jcm.01940-17] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Early establishment of infectious processes allows for expedited clinical management of meningitis and encephalitis. The FilmArray meningitis/encephalitis (FA-M/E) panel provides rapid detection of potential pathogens associated with encephalitis/meningitis in both immunocompetent and compromised patients. Here, we conducted a 1-year review of the performance of the FA-M/E panel at a tertiary care children's hospital. Two hundred sixty-five samples from 251 patients were tested. We found 87.25% (219/251) were negative, 9.96% (25/251) were positive for viral analytes, and 3.19% (8/251) were positive for bacterial analytes. When possible, positive results were confirmed by alternate testing; 4/6 available bacterial positives and 17/20 available viral positives were confirmed by retrospective culture or molecular testing.
Collapse
|
32
|
New Technologies for the Diagnosis of Infection. DIAGNOSTIC PATHOLOGY OF INFECTIOUS DISEASE 2018. [PMCID: PMC7152403 DOI: 10.1016/b978-0-323-44585-6.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
33
|
Khumalo J, Nicol M, Hardie D, Muloiwa R, Mteshana P, Bamford C. Diagnostic accuracy of two multiplex real-time polymerase chain reaction assays for the diagnosis of meningitis in children in a resource-limited setting. PLoS One 2017; 12:e0173948. [PMID: 28346504 PMCID: PMC5367690 DOI: 10.1371/journal.pone.0173948] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/01/2017] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Accurate etiological diagnosis of meningitis is important, but difficult in resource-limited settings due to prior administration of antibiotics and lack of viral diagnostics. We aimed to develop and validate 2 real-time multiplex PCR (RT-PCR) assays for the detection of common causes of community-acquired bacterial and viral meningitis in South African children. METHODS We developed 2 multiplex RT- PCRs for detection of S. pneumoniae, N. meningitidis, H. influenzae, enteroviruses, mumps virus and herpes simplex virus. We tested residual CSF samples from children presenting to a local paediatric hospital over a one-year period, whose CSF showed an abnormal cell count. Results were compared with routine diagnostic tests and the final discharge diagnosis. We calculated accuracy of the bacterial RT-PCR assay compared to CSF culture and using World Health Organisation definitions of laboratory-confirmed bacterial meningitis. RESULTS From 292 samples, bacterial DNA was detected in 12 (4.1%) and viral nucleic acids in 94 (32%). Compared to CSF culture, the sensitivity and specificity of the bacterial RT-PCR was 100% and 97.2% with complete agreement in organism identification. None of the cases positive by viral RT-PCR had a bacterial cause confirmed on CSF culture. Only 9/90 (10%) of patients diagnosed clinically as bacterial meningitis or partially treated bacterial meningitis tested positive with the bacterial RT-PCR. DISCUSSION In this population the use of 2 multiplex RT-PCRs targeting 6 common pathogens gave promising results. If introduced into routine diagnostic testing, these multiplex RT-PCR assays would supplement other diagnostic tests, and have the potential to limit unnecessary antibiotic therapy and hospitalisation.
Collapse
MESH Headings
- Bacteria/genetics
- Bacteria/isolation & purification
- Child
- Child, Preschool
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- Enterovirus/genetics
- Enterovirus/isolation & purification
- Female
- Haemophilus influenzae/genetics
- Haemophilus influenzae/isolation & purification
- Humans
- Male
- Meningitis, Bacterial/cerebrospinal fluid
- Meningitis, Bacterial/diagnosis
- Meningitis, Bacterial/epidemiology
- Meningitis, Bacterial/microbiology
- Meningitis, Viral/cerebrospinal fluid
- Meningitis, Viral/diagnosis
- Meningitis, Viral/epidemiology
- Meningitis, Viral/virology
- Multiplex Polymerase Chain Reaction/methods
- Mumps virus/genetics
- Mumps virus/isolation & purification
- Neisseria meningitidis/genetics
- Neisseria meningitidis/isolation & purification
- Nucleic Acids/genetics
- Nucleic Acids/isolation & purification
- Sensitivity and Specificity
- Simplexvirus/genetics
- Simplexvirus/isolation & purification
- South Africa
- Streptococcus pneumoniae/genetics
- Streptococcus pneumoniae/isolation & purification
- Viruses/genetics
- Viruses/isolation & purification
Collapse
Affiliation(s)
- Jermaine Khumalo
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark Nicol
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Diana Hardie
- National Health Laboratory Service, Johannesburg, South Africa
- Division of Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Rudzani Muloiwa
- Department of Paediatrics, University of Cape Town, Cape Town, South Africa
| | - Phindile Mteshana
- Department of Paediatrics, University of Cape Town, Cape Town, South Africa
| | - Colleen Bamford
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Johannesburg, South Africa
- * E-mail:
| |
Collapse
|
34
|
Berger JR, Wilson MR. Next-generation sequencing of tissue: A logical extension. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2016; 3:e261. [PMID: 27458600 PMCID: PMC4946770 DOI: 10.1212/nxi.0000000000000261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Joseph R Berger
- Department of Neurology (J.R.B.), Perelman School of Medicine, University of Pennsylvania, Philadelphia; and the Department of Neurology (M.R.W.), University of California San Francisco
| | - Michael R Wilson
- Department of Neurology (J.R.B.), Perelman School of Medicine, University of Pennsylvania, Philadelphia; and the Department of Neurology (M.R.W.), University of California San Francisco
| |
Collapse
|