1
|
Chen J, Qin Z, Jia Z. The application status of sequencing technology in global respiratory infectious disease diagnosis. Infection 2024:10.1007/s15010-024-02360-4. [PMID: 39152290 DOI: 10.1007/s15010-024-02360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Next-generation sequencing (NGS) has revolutionized clinical microbiology, particularly in diagnosing respiratory infectious diseases and conducting epidemiological investigations. This narrative review summarizes conventional methods for routine respiratory infection diagnosis, including culture, smear microscopy, immunological assays, image techniques as well as polymerase chain reaction(PCR). In contrast to conventional methods, there is a new detection technology, sequencing technology, and here we mainly focus on the next-generation sequencing NGS, especially metagenomic NGS(mNGS). NGS offers significant advantages over traditional methods. Firstly, mNGS eliminates assumptions about pathogens, leading to faster and more accurate results, thus reducing diagnostic time. Secondly, it allows unbiased identification of known and novel pathogens, offering broad-spectrum coverage. Thirdly, mNGS not only identifies pathogens but also characterizes microbiomes, analyzes human host responses, and detects resistance genes and virulence factors. It can complement targeted sequencing for bacterial and fungal classification. Unlike traditional methods affected by antibiotics, mNGS is less influenced due to the extended survival of pathogen DNA in plasma, broadening its applicability. However, barriers to full integration into clinical practice persist, primarily due to cost constraints and limitations in sensitivity and turnaround time. Despite these challenges, ongoing advancements aim to improve cost-effectiveness and efficiency, making NGS a cornerstone technology for global respiratory infection diagnosis.
Collapse
Affiliation(s)
- Jingyuan Chen
- Department of Global Health, School of Public Health, Peking University, Beijing, China
| | - Zhen Qin
- School of Public Health, Peking University, Beijing, China
| | - Zhongwei Jia
- Department of Global Health, School of Public Health, Peking University, Beijing, China.
- Center for Intelligent Public Health, Institute for Artificial Intelligence, Peking University, Beijing, China.
- Center for Drug Abuse Control and Prevention, National Institute of Health Data Science, Peking University, Beijing, China.
| |
Collapse
|
2
|
Zhang L, Fang K, Ren H, Fan S, Wang J, Guan H. Comparison of the diagnostic significance of cerebrospinal fluid metagenomic next-generation sequencing copy number variation analysis and cytology in leptomeningeal malignancy. BMC Neurol 2024; 24:223. [PMID: 38943096 PMCID: PMC11212224 DOI: 10.1186/s12883-024-03655-7] [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: 01/14/2024] [Accepted: 04/26/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Diagnosis and monitoring of leptomeningeal malignancy remain challenging, and are usually based on neurological, radiological, cerebrospinal fluid (CSF) and pathological findings. This study aimed to investigate the diagnostic performance of CSF metagenomic next-generation sequencing (mNGS) and chromosome copy number variations (CNVs) analysis in the detection of leptomeningeal malignancy. METHODS Of the 51 patients included in the study, 34 patients were diagnosed with leptomeningeal malignancies, and 17 patients were diagnosed with central nervous system (CNS) inflammatory diseases. The Sayk's spontaneous cell sedimentation technique was employed for CSF cytology. And a well-designed approach utilizing the CSF mNGS-CNVs technique was explored for early diagnosis of leptomeningeal malignancy. RESULTS In the tumor group, 28 patients were positive for CSF cytology, and 24 patients were positive for CSF mNGS-CNVs. Sensitivity and specificity of CSF cytology were 82.35% (95% CI: 66.83-92.61%) and 94.12% (95% CI: 69.24-99.69%). In comparison, sensitivity and specificity of CSF mNGS-CNV were 70.59% (95% CI: 52.33-84.29%) and 100% (95% CI: 77.08-100%). There was no significant difference in diagnostic consistency between CSF cytology and mNGS-CNVs (p = 0.18, kappa = 0.650). CONCLUSIONS CSF mNGS-CNVs tend to have higher specificity compared with traditional cytology and can be used as a complementary diagnostic method for patients with leptomeningeal malignancies.
Collapse
Affiliation(s)
- Le Zhang
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Kechi Fang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, 100101, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haitao Ren
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Siyuan Fan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jing Wang
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, 100101, China.
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hongzhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| |
Collapse
|
3
|
Osborn LJ, Fissel J, Gomez S, Mestas J, Flores-Vazquez J, Lee J, Hakimjavadi H, Costales C, Dien Bard J. Development of an automated amplicon-based next-generation sequencing pipeline for rapid detection of bacteria and fungi directly from clinical specimens. J Clin Microbiol 2024; 62:e0174923. [PMID: 38624235 PMCID: PMC11077995 DOI: 10.1128/jcm.01749-23] [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: 12/29/2023] [Accepted: 03/23/2024] [Indexed: 04/17/2024] Open
Abstract
The timely identification of microbial pathogens is essential to guide targeted antimicrobial therapy and ultimately, successful treatment of an infection. However, the yield of standard microbiology testing (SMT) is directly related to the duration of antecedent antimicrobial therapy as SMT culture methods are dependent on the recovery of viable organisms, the fastidious nature of certain pathogens, and other pre-analytic factors. In the last decade, metagenomic next-generation sequencing (mNGS) has been successfully utilized as a diagnostic tool for various applications within the clinical laboratory. However, mNGS is resource, time, and labor-intensive-requiring extensive laborious preliminary benchwork, followed by complex bioinformatic analysis. We aimed to address these shortcomings by developing a largely Automated targeted Metagenomic next-generation sequencing (tmNGS) PipeLine for rapId inFectIous disEase Diagnosis (AMPLIFIED) to detect bacteria and fungi directly from clinical specimens. Therefore, AMPLIFIED may serve as an adjunctive approach to complement SMT. This tmNGS pipeline requires less than 1 hour of hands-on time before sequencing and less than 2 hours of total processing time, including bioinformatic analysis. We performed tmNGS on 50 clinical specimens with concomitant cultures to assess feasibility and performance in the hospital laboratory. Of the 50 specimens, 34 (68%) were from true clinical infections. Specimens from cases of true infection were more often tmNGS positive compared to those from the non-infected group (82.4% vs 43.8%, respectively, P = 0.0087). Overall, the clinical sensitivity of AMPLIFIED was 54.6% with 85.7% specificity, equating to 70.6% and 75% negative and positive predictive values, respectively. AMPLIFIED represents a rapid supplementary approach to SMT; the typical time from specimen receipt to identification of potential pathogens by AMPLIFIED is roughly 24 hours which is markedly faster than the days, weeks, and months required to recover bacterial, fungal, and mycobacterial pathogens by culture, respectively. IMPORTANCE To our knowledge, this represents the first application of an automated sequencing and bioinformatics pipeline in an exclusively pediatric population. Next-generation sequencing is time-consuming, labor-intensive, and requires experienced personnel; perhaps contributing to hesitancy among clinical laboratories to adopt such a test. Here, we report a strong case for use by removing these barriers through near-total automation of our sequencing pipeline.
Collapse
Affiliation(s)
- Lucas J. Osborn
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - John Fissel
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Samantha Gomez
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Javier Mestas
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Jessica Flores-Vazquez
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Jaehyeon Lee
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Jeollabukdo, South Korea
| | - Hesamedin Hakimjavadi
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Cristina Costales
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
4
|
Zou Y, Wang L, Li Y, Wu Y, He J, Yu X. A comparison of clinical features between neurobrucellosis and tuberculous meningitis. BMC Neurol 2024; 24:136. [PMID: 38664634 PMCID: PMC11044361 DOI: 10.1186/s12883-024-03631-1] [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: 10/09/2023] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUD This study aims to compare the clinical manifestations, imaging findings, routine tests, biochemistry indicators and cerebrospinal fluid cytology between neurobrucellosis and tuberculous meningitis. The objective is to evaluate the similarities and differences of these two diseases and improve early diagnosis. METHODS A comprehensive evaluation was conducted by comparing clinical data, imaging results, routine tests findings, biochemistry indicators and cerebrospinal fluid cytology of patients admitted to the Department of Neurology, the Second Hospital of Hebei Medical University from 2019 to 2021. Statistical analysis was applied to identify significant differences and similarities between the two diseases. RESULTS Preliminary analysis demonstrated both diseases commonly present with symptoms such as fever, headache. However, there were no statistical differences between neurobrucellosis and tuberculous meningitis in early clinical data, imaging results, routine tests findings, biochemistry indicators. Further analysis indicates there is a statistically significantly difference in the lymphocyte ratio and neutrophil ratio in the cerebrospinal fluid between the two groups. CONCLUSIONS Neurobrucellosis and tuberculous meningitis share similarities in early clinical manifestations, imaging findings and initial cerebrospinal fluid parametes, making early-stage differentiation challenging. The ratio of lymphocytes and neutrophil in the cerebrospinal fluid and a detailed medical history investigation can provide clues for early clinical diagnosis. So the examination of CSF cytology might be a potential to distinguish these two diseases and become a powerful tool in the future.
Collapse
Affiliation(s)
- Yueli Zou
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, PR China
| | - Liqing Wang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, PR China
| | - Yi Li
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, PR China
| | - Yaning Wu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, PR China
| | - Junying He
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, PR China
| | - Xiujun Yu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, PR China.
| |
Collapse
|
5
|
Li W, He Y, Li Y, Li X, Bian T, Liu T, Liu X, Jiang W. Metagenomic next-generation sequencing for the diagnosis of neurobrucellosis. Future Microbiol 2024; 19:509-518. [PMID: 38629898 PMCID: PMC11216504 DOI: 10.2217/fmb-2023-0177] [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: 08/13/2023] [Accepted: 12/06/2023] [Indexed: 06/27/2024] Open
Abstract
Objective: This study investigates the application of metagenomic next-generation sequencing (mNGS) in the diagnosis of neurobrucellosis (NB). Methods: We retrospectively analyzed patients diagnosed with NB who underwent cerebrospinal fluid (CSF) mNGS testing in Xijing Hospital from 2015 to 2021. Results: Among the 20 individuals included in the study, the serum rose bengal test was positive in 11 out of 16 cases, serum agglutination test was positive in 13 out of 16 cases, CSF culture was positive in 6 out of 11 cases, and CSF mNGS tests were positive in 18 out of 20 cases. Conclusion: CSF mNGS demonstrates superior sensitivity; therefore, it is recommended to collect CSF for mNGS testing prior to antibiotic therapy when NB is suspected.
Collapse
Affiliation(s)
- Wen Li
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Ying He
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yanyan Li
- Department of Neurology, Ordnance Industry No. 521 Hospital, Xi'an, China
| | - Xiaona Li
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Ting Bian
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Tingting Liu
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xuedong Liu
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Wen Jiang
- Department of Neurology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| |
Collapse
|
6
|
Jiang J, Lv M, Yang K, Zhao G, Fu Y. A case report of diagnosis and dynamic monitoring of Listeria monocytogenes meningitis with NGS. Open Life Sci 2023; 18:20220738. [PMID: 37954099 PMCID: PMC10638841 DOI: 10.1515/biol-2022-0738] [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: 05/30/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 11/14/2023] Open
Abstract
Listeria monocytogenes (LM) infections of the central nervous system are deadly and have vague symptoms. Traditional cerebro spinal fluid culture has a low positive rate, and because antibiotic use is common following therapy, it is more challenging to assess the response from pathogen content. In this case, a 66-year-old man who had a fever, a headache, and vomit was admitted to the hospital. He had diabetes, decline in thyroid function, and a history of pituitary tumor removal surgery. His initial treatment with ribavirin, ceftriaxone antibiotic, and moxifloxacin did not go well. Using two etiological tests (culture and metagenomic next-generation sequencing [mNGS]), his cerebrospinal fluid tested positively for LM. Ampicillin-sulbactam and meropenem were used as treatments once LM meningitis was identified. After treatment, his cerebrospinal fluid was assessed once more. Culture: negative; targeted next-generation sequencing (tNGS): positive and shows changes in the copy number of the LM. After 44 days of treatment, the patient finally stopped taking antibiotics, and the prognosis was good. Our study showed that mNGS and tNGS, as novel approaches for pathogen detection, are capable of identifying pathogens quickly, sensitively, and accurately, especially when there are few infections present (such as after antibiotic treatment). The two methods can be a powerful assistance for helping clinicians to choose the best course of action.
Collapse
Affiliation(s)
- Jiamei Jiang
- Department of Emergency Medicine, Shanghai Jiaotong University Affiliated Sixth People’ Hospital, No. 600 Yishan Road, Xuhui District, Shanghai200233, China
| | - Meng Lv
- Genoxor Medical Science and Technology Inc., Shanghai201100, China
| | - Kaichao Yang
- Department of Emergency Medicine, Shanghai Jiaotong University Affiliated Sixth People’ Hospital, No. 600 Yishan Road, Xuhui District, Shanghai200233, China
| | - Gang Zhao
- Department of Emergency Medicine, Shanghai Jiaotong University Affiliated Sixth People’ Hospital, No. 600 Yishan Road, Xuhui District, Shanghai200233, China
| | - Yimu Fu
- Department of Emergency Medicine, Shanghai Jiaotong University Affiliated Sixth People’ Hospital, No. 600 Yishan Road, Xuhui District, Shanghai200233, China
| |
Collapse
|
7
|
Yu L, Zhang Z, Zou Y, Qi X, Zhang Y, Bai K, Han X, Bu H. Next-generation sequencing in the diagnosis of neurobrucellosis: a case series of eight consecutive patients. Ann Clin Microbiol Antimicrob 2023; 22:44. [PMID: 37268917 DOI: 10.1186/s12941-023-00596-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/29/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Neurobrucellosis (NB) presents a challenge for rapid and specific diagnosis. Next-generation sequencing (NGS) of cerebrospinal fluid (CSF) has showed power in detection of causative pathogens, even some infrequent and unexpected pathogens. In this study, we presented 8 cases of NB diagnosed by the NGS of CSF. METHODS Between August 1, 2018 and September 30, 2020, NGS was used to detect causative pathogens in clinically suspected central nervous system (CNS) infections. Data on demographics, clinical features, and laboratory tests, imaging results and NGS results were collected and reviewed. RESULTS Among the presented 8 patients, Brucella was rapidly detected using NGS of CSF within 1-4 days, despite those eight patients had variable medical history, disease course, clinical manifestations, laboratory tests and imaging findings. NGS showed the sequence reads corresponded to Brucella species were 8 to 448, with genomic coverage of 0.02 to 0.87%. The relative abundance was 0.13% to 82.40% and sequencing depth was 1.06 to 1.24. Consequently, patients were administered with 3 to 6 months of doxycycline, ceftriaxone and rifampicin, double or triple combination, supplemented with symptomatic therapy and were fully recovered except for case 1. CONCLUSION NGS of CSF provides a powerful tool in detection of Brucella in a prompt and specific manner, and can be considered for first-line diagnostic use in practice.
Collapse
Affiliation(s)
- Lili Yu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Zhenyuan Zhang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Yueli Zou
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Xuejiao Qi
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Yu Zhang
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Kaixuan Bai
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Xiaochen Han
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Hui Bu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China.
| |
Collapse
|
8
|
Abstract
PURPOSE OF REVIEW Brucellosis is one of the most common zoonosis worldwide, affecting 500 000 people, annually. Neurobrucellosis incidence is approximately 4%, and it is almost always heterogeneous. As there are no typical clinical features, its diagnosis is frequently misdiagnosing by other infections. RECENT FINDINGS Neurobrucellosis picture includes meningitis, meningoencephalitis, encephalitis, cranial neuropathies, intracranial hypertension, sinus thrombosis, hemorrhages radiculitis, peripheral neuropathy, myelitis, and psychiatric manifestations. The diagnosis should be based on symptoms and signs suggestive of neurobrucellosis, not explained by other neurological disease, cerebrospinal fluid analysis, a positive Brucella serology or culture, and a response to specific antibiotics, with a significant improvement of cerebrospinal fluid parameters. SUMMARY Neurobrucellosis can be insidious, and despite its global distribution, it is still unrecognized and frequently goes unreported. The understanding of the current epidemiology is necessary for eradication of the disease in humans, as well as the disease control in animals and prevention based on occupational hygiene and food hygiene.
Collapse
Affiliation(s)
- Cristiane N Soares
- Infectious Diseases Department (DIP 1) - Hospital Federal dos Servidores do Estado
| | - Marcus Tulius T da Silva
- Laboratory of Clinical Research in Neuroinfections- Evandro Chagas National Institute of Infectious Diseases (INI) - FIOCRUZ
| | - Marco Antonio Lima
- Fundação Oswaldo Cruz, Universidade Federal do Rio de Janeiro, RJ, Brazil
| |
Collapse
|
9
|
Estagnasié C, Surgers L, Berdugo K, Monnier-Cholley L, Schmidt M, Meynard JL, Gras E. Recurrence of brucellosis on breast implants. Infect Dis Now 2023; 53:104644. [PMID: 36642098 DOI: 10.1016/j.idnow.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/12/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023]
Affiliation(s)
- C Estagnasié
- GHU APHP. Sorbonne Université, Service des maladies infectieuses et tropicales, Hôpital Saint-Antoine, F75012 Paris, France
| | - L Surgers
- GHU APHP. Sorbonne Université, Service des maladies infectieuses et tropicales, Hôpital Saint-Antoine, F75012 Paris, France; Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique, F75012 Paris, France
| | - K Berdugo
- GHU APHP. Sorbonne Université, Service des maladies infectieuses et tropicales, Hôpital Saint-Antoine, F75012 Paris, France
| | - L Monnier-Cholley
- GHU APHP. Sorbonne Université, Service de radiologie, Hôpital Saint-Antoine, F75012 Paris, France
| | - M Schmidt
- GHU APHP. Sorbonne Université, Service de chirurgie plastique reconstructive et esthétique, Hôpital Tenon, F75020 Paris, France
| | - J-L Meynard
- GHU APHP. Sorbonne Université, Service des maladies infectieuses et tropicales, Hôpital Saint-Antoine, F75012 Paris, France
| | - E Gras
- GHU APHP. Sorbonne Université, Service des maladies infectieuses et tropicales, Hôpital Saint-Antoine, F75012 Paris, France; Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique, F75012 Paris, France.
| |
Collapse
|
10
|
Liu Y, Mo X, Feng Y, Willoughby RE, Weng X, Wang Y, Li X, Gao J, Tian J, Peng J. Metagenomic next-generation sequencing for the etiological diagnosis of rabies virus in cerebrospinal fluid. Front Med (Lausanne) 2023; 10:982290. [PMID: 36844226 PMCID: PMC9947348 DOI: 10.3389/fmed.2023.982290] [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: 07/09/2022] [Accepted: 01/02/2023] [Indexed: 02/11/2023] Open
Abstract
Background Rabies is a highly fatal disease. Once symptoms develop, death usually occurs within days. Survivors were occasionally reported in the literatures. Ante-mortem diagnosis remains a challenge in most rabies endemic countries. A novel, accurate diagnostic assay is highly desirable. Methods We used metagenomic next-generation sequencing (mNGS) to examine the cerebrospinal fluid (CSF) samples of a 49-year-old patient with rabies and validated the results by TaqMan PCR and RT-PCR/Sanger sequencing. Results Metagenomic next-generation sequencing identified sequence reads uniquely aligned to the rabies virus (RABV). PCR confirmed the presence of the partial RABV N gene in the CSF. Phylogenetic analysis showed that the RABV grouped as an Asian clade, which is the most broadly distributed clade in China. Conclusion Metagenomic next-generation sequencing may be a useful screening tool for the etiological diagnosis of rabies, especially in the absence of timely rabies laboratory testing or in patients with no exposure history.
Collapse
Affiliation(s)
- Yong Liu
- Intensive Care Unit, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Xichao Mo
- Department of Infectious Diseases, Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Ye Feng
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Rodney E. Willoughby
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, MI, United States
| | - Xing Weng
- Department of Infectious Disease, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yuyang Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Xing Li
- Department of Infectious Disease, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Junling Gao
- Centre of Buddhists Studies, The University of Hong Kong, Hong Kong, Hong Kong SAR, China,Department of Medicine, LKS Medical Faculty, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jinfei Tian
- Intensive Care Unit, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Jie Peng
- Department of Infectious Diseases, Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong, China,*Correspondence: Jie Peng,
| |
Collapse
|
11
|
The Clinical Impact of Metagenomic Next-Generation Sequencing (mNGS) Test in Hospitalized Patients with Suspected Sepsis: A Multicenter Prospective Study. Diagnostics (Basel) 2023; 13:diagnostics13020323. [PMID: 36673134 PMCID: PMC9857658 DOI: 10.3390/diagnostics13020323] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/28/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Background: Metagenomic Next Generation Sequencing (mNGS) has the potential to detect pathogens rapidly. We aimed to assess the diagnostic performance of mNGS in hospitalized patients with suspected sepsis and evaluate its role in guiding antimicrobial therapy. Methods: A multicenter, prospective cohort study was performed. We enrolled patients with suspected sepsis, collected clinical characteristics and blood samples, and recorded the 30-day survival. Diagnostic efficacy of mNGS test and blood culture was compared, and the clinical impact of mNGS on antibiotic regimen modification was analyzed. Results: A total of 277 patients were enrolled, and 162 were diagnosed with sepsis. The mortality was 44.8% (121/270). The mNGS test exhibited shorter turn-out time (27.0 (26.0, 29.0) vs. 96.0 (72.0, 140.3) hours, p < 0.001) and higher sensitivity (90.5% vs. 36.0%, p < 0.001) compared with blood culture, especially for fungal infections. The mNGS test showed better performance for patients with mild symptoms, prior antibiotic use, and early stage of infection than blood culture, and was capable of guiding antibiotic regimen modification and improving prognosis. Higher reads of pathogens detected by mNGS were related to 30-day mortality (p = 0.002). Conclusions: Blood mNGS testing might be helpful for early etiological diagnosis of patients with suspected sepsis, guiding the antibiotic regimen modification and improving prognosis.
Collapse
|
12
|
Yu L, Zhang Y, Qi X, Bai K, Zhang Z, Bu H. Next-generation sequencing for the diagnosis of Listeria monocytogenes meningoencephalitis: a case series of five consecutive patients. J Med Microbiol 2023; 72. [PMID: 36748504 DOI: 10.1099/jmm.0.001641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Introduction. The prompt and specific diagnosis of Listeria monocytogenes meningoencephalitis (LMM) is challenging. Next-generation sequencing (NGS) of cerebrospinal fluid (CSF) is an emerging technique for diagnosing infrequent causative pathogens.Hypothesis/Gap statement. We hypothesized that NGS of CSF is an effective approach for diagnosing LMM.Aim. To evaluate the effectiveness of NGS, we present five cases of LMM diagnosed using NGS of the CSF.Methodology. Between August 2017 and 30 September 2020, we used NGS of the CSF to detect pathogens in patients with clinically suspected central nervous system infections. The clinical characteristics, laboratory tests, imaging findings and NGS results are reviewed.Results. Five patients were diagnosed with LMM using NGS of the CSF within 2 to 4 days, although the clinical manifestations, medical history and imaging findings varied strikingly. NGS of CSF showed sequence reads corresponding to L. monocytogenes species ranging from 118 to 1997 bp, genomic coverage of 0.29-5.96 %, relative abundance of 14.83-32.16 % and sequencing depth of 1.12 to 1.35. The prompt diagnosis resulted in targeted and effective treatment with the appropriate antibiotics, although two patients with the most severe cerebral parenchymal lesions showed little improvement.Conclusion. Our results demonstrate the power of NGS of CSF for the prompt diagnosis of LMM. NGS of CSF is an important complementary tool for identifying L. monocytogenes.
Collapse
Affiliation(s)
- Lili Yu
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
| | - Yu Zhang
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
| | - Xuejiao Qi
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
| | - Kaixuan Bai
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
| | - Zhenyuan Zhang
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
| | - Hui Bu
- Department of Neurology, the Second Hospital of Hebei Medical University, Shijiazhuang 050000, Hebei, PR China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang 050000, Hebei, PR China
| |
Collapse
|
13
|
Li X, Liang S, Zhang D, He M, Zhang H. The clinical application of metagenomic next-generation sequencing in sepsis of immunocompromised patients. Front Cell Infect Microbiol 2023; 13:1170687. [PMID: 37168393 PMCID: PMC10164957 DOI: 10.3389/fcimb.2023.1170687] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/27/2023] [Indexed: 05/13/2023] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) was commonly applied given its ability to identify and type all infections without depending upon culture and to retrieve all DNA with unbiasedness. In this study, we strive to compare outcomes of mNGS with conventional culture methods in adults with sepsis, investigate the differences between the immunocompromised and control group, and assess the clinical effects of mNGS. Methods In our study, 308 adult sepsis patients were included. We used both mNGS and conventional culture methods to analyze diagnostic results, pathogens, and sample types. The correlation between some laboratory tests and the frequency of pathogens by groups was also analyzed. Furthermore, the clinical impacts of mNGS were estimated. Results 308 samples were assigned to an immunocompromised group (92/308,29.9%) and a control group (216/308,70.1%). There was the sensitivity of mNGS considered greater than that of the culture method in all samples (88.0% vs 26.3%; P < 0.001), in the immunocompromised group (91.3% vs 26.1%; P < 0.001), and the control group (86.6% vs 26.4%; P < 0.001), particularly in all sample types of blood (P < 0.001), BALF (P < 0.001), CSF (P < 0.001), sputum (P < 0.001) and ascitic fluid (P = 0.008). When examining the mNGS results between groups, Pneumocystis jirovecii (P < 0.001), Mucoraceae (P = 0.014), and Klebsiella (P = 0.045) all showed significant differences. On the whole, mNGS detected more pathogens than culture methods (111 vs 25), found 89 organisms that were continuously overlooked in entire samples by culture methods, and showed a favorable positive clinical effect in 76.3% (235 of 308) of patients. In 185 (60.1%) patients, mNGS prompted a modification in the course of management, which included antibiotic de-escalation in 61(19.8%) patients. Conclusions The research discovered that mNGS was more sensitive than the culture method, particularly in samples of blood, BALF, CSF, sputum, and ascitic fluid. When examining the mNGS results, Pneumocystis jirovecii and Mucoraceae were the pathogens seen more commonly in immunocompromised patients with sepsis, which required more attention from clinicians. There was a substantial benefit of mNGS in enhancing the diagnosis of sepsis and advancing patient treatment.
Collapse
|
14
|
Zhang Q, Liu X, Liu Y, Wang H, Zhao R, Lv X, Wei X, Zhou K. Nasal and cutaneous mucormycosis in two patients with lymphoma after chemotherapy and target therapy: Early detection by metagenomic next-generation sequencing. Front Cell Infect Microbiol 2022; 12:960766. [PMID: 36189372 PMCID: PMC9524479 DOI: 10.3389/fcimb.2022.960766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/25/2022] [Indexed: 11/25/2022] Open
Abstract
Mucormycosis is a conditionally pathogenic fungal disease with high morbidity that mainly affects patients with decreased immunity. Diagnosis relies on the histopathological examination of microorganisms with the typical structure of mucormycetes in tissues and subsequent confirmation via culture. Early detection of causative microorganisms is critical to rapidly administer appropriately targeted antibiotics. Metagenomic next-generation sequencing (mNGS) is an innovative and sensitive technique used to identify pathogenic strains. Here we used mNGS to timely diagnose an infection with Lichtheimia ramosa and Mucor irregularis in two patients with hematologic malignancies; the infections manifested as nasal and cutaneous infections and developed after chemotherapy and small molecule targeted therapy. Following treatment with amphotericin B cholesteryl sulfate complex, the symptoms were reduced significantly, and both patients obtained successful outcomes. Additionally, we searched and summarized the current medical literature on the successful diagnosis of mucormycosis using mNGS. These cases indicated that mNGS, a novel culture-independent method, is capable of rapid, sensitive, and accurate identification of pathogens. mNGS may be a complementary method for the early identification of mucormycosis, allowing for appropriate and timely antibiotic administration and thus improving patient outcomes.
Collapse
|
15
|
Zoghi S, Masoudi MS, Taheri R. The Evolving Role of Next Generation Sequencing in Pediatric Neurosurgery: a Call for Action for Research, Clinical Practice, and Optimization of Care. World Neurosurg 2022; 168:232-242. [PMID: 36122859 DOI: 10.1016/j.wneu.2022.09.056] [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: 07/10/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Abstract
NGS (Next-Generation Sequencing) is one of the most promising technologies that have truly revolutionized many aspects of clinical practice in recent years. It has been and is increasingly applied in many disciplines of medicine; however, it appears that pediatric neurosurgery despite its great potential has not truly embraced this new technology and is hesitant to employ it in its routine practice and guidelines. In this review, we briefly summarized the developments that lead to the establishment of NGS technology, reviewed the current applications and potentials of NGS in the disorders treated by pediatric neurosurgeons, and lastly discuss the steps we need to take to better harness NGS in pediatric neurosurgery.
Collapse
Affiliation(s)
- Sina Zoghi
- Department of Neurosurgery, Shiraz University of Medical Sciences, Shiraz, Iran; Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Reza Taheri
- Department of Neurosurgery, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
16
|
Dong Y, He Y, Zhou X, Lv X, Huang J, Li Y, Qian X, Hu F, Zhu J. Diagnosis of Mycoplasma hominis Meningitis with Metagenomic Next-Generation Sequencing: A Case Report. Infect Drug Resist 2022; 15:4479-4486. [PMID: 35983300 PMCID: PMC9380824 DOI: 10.2147/idr.s371771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
Background Mycoplasma hominis meningitis is a rare postoperative complication of neurosurgery. Accurate and early diagnosis of M. hominis remains challenging because of the limitations of traditional detection methods. Metagenomic next-generation sequencing (mNGS) is an advanced technique with high sensitivity and specificity for identifying infectious pathogens; however, its application in diagnosing M. hominis meningitis has not been widely studied. Case Presentation We report the case of a 61-year-old man who presented with fever and headache after neurosurgical treatment for a cerebral hemorrhage. Empiric antibiotic therapy was ineffective. Traditional culture of pathogens and serological testing yielded negative results, but M. hominis was detected in the cerebrospinal fluid by mNGS. After further verification by polymerase chain reaction (PCR), the patient's clinical treatment was adjusted accordingly. With targeted antibiotic intervention, the patient's symptoms were effectively alleviated, and clinical indicators returned to normal levels. Furthermore, the abundance of M. hominis decreased significantly compared to the initial mNGS reading after targeted treatment, indicating that the infection caused by M. hominis was effectively controlled. Conclusion Using mNGS, we found that M. hominis may be a candidate causative agent of meningitis. The technique also has the advantage of timeliness and accuracy that traditional cultures cannot achieve. A combination of mNGS with PCR is recommended to identify pathogens in the early stages of infectious diseases to administer targeted clinical medication.
Collapse
Affiliation(s)
- Yukang Dong
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Yingying He
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Xia Zhou
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Xia Lv
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Jia Huang
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Yaqi Li
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Xin Qian
- Department of Pharmacy, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Fangfang Hu
- Department of Clinical Laboratory, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| | - Jiaying Zhu
- Department of Emergency, Guizhou Provincial People's Hospital, Guiyang, People's Republic of China
| |
Collapse
|
17
|
Xi Y, Zhou J, Lin Z, Liang W, Yang C, Liu D, Xu Y, Nong L, Chen S, Yu Y, He W, Zhang J, Zhang R, Liu X, Liu X, Sang L, Xu Y, Li Y. Patients with infectious diseases undergoing mechanical ventilation in the intensive care unit have better prognosis after receiving metagenomic next-generation sequencing assay. Int J Infect Dis 2022; 122:959-969. [PMID: 35908725 DOI: 10.1016/j.ijid.2022.07.062] [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: 02/15/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 10/16/2022] Open
Abstract
OBJECTIVES To evaluate the relation between mNGS and the prognosis of patients with infectious diseases undergoing mechanical ventilation in the intensive care unit (ICU). DESIGN This is a single-center observational study, comparing non-randomly assigned diagnostic approaches. We analyzed the medical records of 228 patients with suspected infectious diseases undergoing mechanical ventilation in the ICU from March 2018 to May 2020. The concordance of pathogen results was also assessed for the results of mNGS, culture and PCR assays. RESULTS The 28-day mortality of the patients in the mNGS group was lower after the baseline difference correction (19.23% (20/104) vs. 29.03% (36/124) , p=0.039). Subgroup analysis showed that mNGS assay associates with improved 28-day mortality of non-immunosuppressive patients (14.06% vs. 29.82%, p=0.018) . Not performing mNGS assay, higher APACHE II score and hypertension are independent risk factors for 28-day mortality. The mNGS assay presented advantage in pathogen positivity (69.8% double positive and 25.0% mNGS positive only), and the concordance between thest two assays were 79.0%. CONCLUSIONS mNGS survey may be associated with a better prognosis as the reduction of 28-day mortality of patients with infectious diseases on mechanical ventilation in ICU. This technique presented advantage in pathogen positivity than traditional methods.
Collapse
Affiliation(s)
- Yin Xi
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Jing Zhou
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Zhimin Lin
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Weibo Liang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Chun Yang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Dongdong Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Yonghao Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Lingbo Nong
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Sibei Chen
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Yuheng Yu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Weiqun He
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Jie Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Rong Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Xuesong Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Xiaoqing Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China
| | - Ling Sang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China..
| | - Yuanda Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China..
| | - Yimin Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Department of Pulmonary and Critical Care Medicine, 151 Yanjiang Road, Guangzhou, 510120, China..
| |
Collapse
|
18
|
Wu W, Jiang H, Zhang Y, Zhou Y, Bai G, Shen L, Zhou H, Chen X, Hu L. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Secondary Glaucoma in Patients With Cytomegalovirus-Induced Corneal Endotheliitis. Front Microbiol 2022; 13:940818. [PMID: 35865935 PMCID: PMC9295740 DOI: 10.3389/fmicb.2022.940818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
Glaucoma is the second leading cause of blindness globally. Growing scientific evidence indicated that inflammation of the trabecular meshwork induced by corneal endotheliitis could lead to secondary glaucoma. Cytomegalovirus (CMV) has been identified as the most common herpes virus in corneal endotheliitis patients. Early detection is critical in preventing endothelial cell loss, and patient management should vary based on different pathological factors. However, routine culture and real-time polymerase chain reaction (qPCR) have difficult in distinguishing whether CMV, Varicella Zoster Virus (VZV) or Herpes Simplex Virus (HSV) causes endothiliitis. This may result in inappropriate treatment, which may prolong or aggravate the status of disease. We compared the sensitivity and specificity of qPCR and Metagenomic Next-Generation Sequencing (mNGS) in the aqueous humor of patients with suspected CMV endotheliitis in this study. Our results showed that four out of 11 (36.4%) of our patients were positive for CMV by qPCR, whereas mNGS had a 100% detection rate of CMV. Our findings implied that mNGS could be a useful diagnostic tool for CMV-induced endotheliitis.
Collapse
Affiliation(s)
- Wei Wu
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hua Jiang
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Zhang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yang Zhou
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd., Hangzhou, China
| | - Guannan Bai
- The Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingwei Shen
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Hongwei Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangjun Chen
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Xiangjun Chen,
| | - Lidan Hu
- The Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
- Lidan Hu,
| |
Collapse
|
19
|
Zhang X, Li Y, Yin J, Xi B, Wang N, Zhang Y. Application of Next-Generation Sequencing in Infections After Allogeneic Haematopoietic Stem Cell Transplantation: A Retrospective Study. Front Cell Infect Microbiol 2022; 12:888398. [PMID: 35774403 PMCID: PMC9239075 DOI: 10.3389/fcimb.2022.888398] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
This retrospective study aimed to determine the characteristics of infection and diagnostic efficacy of next-generation sequencing (NGS) in patients with fever after allogeneic hematopoietic stem cell transplantation (allo-HSCT). A total of 71 patients with fever after HSCT were enrolled in this study. Compared with conventional microbiological test (CMT), we found that the sensitivity of NGS versus CMT in peripheral blood samples was 91.2% vs. 41.2%, and that NGS required significantly less time to identify the pathogens in both monomicrobial infections (P=0.0185) and polymicrobial infections (P= 0.0027). The diagnostic performance of NGS was not affected by immunosuppressant use. Viruses are the most common pathogens associated with infections. These results indicated that the sensitivity, timeliness, and clinical significance of NGS are superior for the detection of infections. Although NGS has the advantage of identifying a wide range of potential pathogens, the positive rate is related closely to the sample type. Therefore, we recommend that, in the clinical application of NGS to detect pathogens in patients after allo-HSCT, an appropriate sample type and time should be selected and submitted to improve the positive rate and accuracy of NGS. NGS holds promise as a powerful technology for the diagnosis of fever after HSCT.
Collapse
Affiliation(s)
- Xiaoying Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jin Yin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bixin Xi
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Na Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yicheng Zhang, ; Na Wang,
| | - Yicheng Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yicheng Zhang, ; Na Wang,
| |
Collapse
|
20
|
Li CX, Burrell R, Dale RC, Kesson A, Blyth CC, Clark JE, Crawford N, Jones CA, Britton PN, Holmes EC. Diagnosis and analysis of unexplained cases of childhood encephalitis in Australia using metatranscriptomic sequencing. J Gen Virol 2022; 103. [PMID: 35486523 DOI: 10.1099/jgv.0.001736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Encephalitis is most often caused by a variety of infectious agents identified through diagnostic tests utilizing cerebrospinal fluid. We investigated the clinical characteristics and potential aetiological agents of unexplained encephalitis through metagenomic sequencing of residual clinical samples from multiple tissue types and independent clinical review. Forty-three specimens were collected from 18 encephalitis cases with no cause identified by the Australian Childhood Encephalitis study. Samples were subjected to total RNA sequencing ('metatranscriptomics') to determine the presence and abundance of potential pathogens, and to describe the possible aetiologies of unexplained encephalitis. Using this protocol, we identified five RNA and two DNA viruses associated with human infection from both non-sterile and sterile sites, which were confirmed by PCR. These comprised two human rhinoviruses, two human seasonal coronaviruses, two polyomaviruses and one picobirnavirus. Human rhinovirus and seasonal coronaviruses may be responsible for five of the encephalitis cases. Immune-mediated encephalitis was considered likely in six cases and metatranscriptomics did not identify a possible pathogen in these cases. The aetiology remained unknown in nine cases. Our study emphasizes the importance of respiratory viruses in the aetiology of unexplained child encephalitis and suggests that non-central-nervous-system sampling in encephalitis clinical guidelines and protocols could improve the diagnostic yield.
Collapse
Affiliation(s)
- Ci-Xiu Li
- School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia
| | - Rebecca Burrell
- Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Russell C Dale
- Kids Neuroscience Centre, Children's Hospital at Westmead Clinical School, Faculty of Medicine, University of Sydney, NSW, Australia
| | - Alison Kesson
- Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Christopher C Blyth
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute and School of Medicine, University of Western Australia, Nedlands, WA, Australia.,Department of Infectious Diseases, Perth Children's Hospital, Nedlands, WA, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands, WA, Australia
| | - Julia E Clark
- Infection Management, Queensland Children's Hospital, Brisbane, QLD, Australia.,School of Clinical Medicine, Childrens Health Queensland Clinical Unit, University of Queensland, QLD, Australia
| | - Nigel Crawford
- Murdoch Children's Research Institute, Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia
| | - Cheryl A Jones
- Kids Research, Sydney Children's Hospitals Network (Westmead), Westmead, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Philip N Britton
- Kids Research, Sydney Children's Hospitals Network (Westmead), Westmead, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Edward C Holmes
- School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia
| |
Collapse
|
21
|
Soares CN, Angelim AIM, Brandão CO, Santos RQ, Mehta R, Silva MTTD. Neurobrucellosis: the great mimicker. Rev Soc Bras Med Trop 2022; 55:e05672021. [PMID: 35416876 PMCID: PMC9009883 DOI: 10.1590/0037-8682-0567-2021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/25/2022] [Indexed: 11/22/2022] Open
Abstract
Neurobrucellosis is caused by bacteria of the genus Brucella and is responsible for several clinical manifestations, making diagnosis challenging. The most common route of infection is through the consumption of unpasteurized or raw dairy products such as fresh milk, butter, and cheese. As neurological complications can develop chronically, they are frequently misdiagnosed as other infections, such as tuberculosis. This report reviews the clinical manifestations, diagnostic approach, treatment, and prognosis of neurobrucellosis, illustrating a case of chronic intracranial hypertension and meningoencephalitis secondary to brucellosis. The clinical presentation of brucellosis can mimic several systemic diseases, resulting in diagnostic delays and clinical complications. A high degree of suspicion is required, and neurobrucellosis should always be considered in the differential diagnosis of chronic meningitis.
Collapse
Affiliation(s)
| | | | | | - Roberto Queiroz Santos
- Hospital Federal dos Servidores do Estado, Departamento de Radiologia, Rio de Janeiro, RJ, Brasil
| | - Ravi Mehta
- Imperial College London, Department of Infectious Diseases, London, England
| | - Marcus Tulius Teixeira da Silva
- Instituto de Doenças Infecciosas Evandro Chagas, Laboratório de Pesquisa Clínica em Neuroinfecções, Rio de Janeiro, RJ, Brasil
| |
Collapse
|
22
|
Yang H, Wang Z, Shi S, Yu Q, Liu M, Zhang Z. Identification of cerebrospinal fluid metabolites as biomarkers for neurobrucellosis by liquid chromatography-mass spectrometry approach. Bioengineered 2022; 13:6996-7010. [PMID: 35249459 PMCID: PMC8974019 DOI: 10.1080/21655979.2022.2037954] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Neurobrucellosis is the most morbid form in brucellosis disease. Metabolomics is an emerging method which intends to explore the global alterations of various metabolites in samples. We aimed to identify metabolites in cerebrospinal fluid (CSF) as biomarkers that were potentially unique for neurobrucellosis. CSF samples from 25 neurobrucellosis patients and 25 normal controls (uninfected patients with hydrocephalus) were collected for metabolite detection using liquid chromatography-mass spectrometry (LC-MS) approach. Inflammatory cytokines in CSF were measured with Enzyme-linked immunosorbent assay (ELISA). The base peak chromatogram in CSF samples showed that small-molecule metabolites were well separated. Principal Component Analysis (PCA) analysis exhibited the examined samples were arranged in two main clusters in accordance with their group. Projection to Latent Structures Discriminant Analysis (PLS-DA) revealed there was a noticeable separation between neurobrucellosis and normal groups. Orthogonal Partial Least-Squares-Discriminant Analysis (OPLS-DA) could responsibly illuminate the differences between neurobrucellosis and normal controls. Neurobrucellosis showed a total of 155 differentiated metabolites. Prominent potential biomarkers including 30 metabolites were then selected out, regarded as more capable of distinguishing neurobrucellosis. TNF-α and IL-6 in CSF were remarkably increased in neurobrucellosis. We presented the heatmaps and correlation analyses among the identified 30 potential biomarkers. In conclusion, this study showed that CSF metabolomics based on LC-MS could distinguish neurobrucellosis patients from normal controls. Our data offered perspectives for diagnosis and treatment for neurobrucellosis.
Collapse
Affiliation(s)
- Hao Yang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Zhenfei Wang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Shujun Shi
- Department of Neurology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Qin Yu
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital & Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Meiling Liu
- Department of Neurology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Zhelin Zhang
- Department of Neurology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| |
Collapse
|
23
|
Woerner J, Huang Y, Hutter S, Gurnari C, Sánchez JMH, Wang J, Huang Y, Schnabel D, Aaby M, Xu W, Thorat V, Jiang D, Jha BK, Koyuturk M, Maciejewski JP, Haferlach T, LaFramboise T. Circulating microbial content in myeloid malignancy patients is associated with disease subtypes and patient outcomes. Nat Commun 2022; 13:1038. [PMID: 35210415 PMCID: PMC8873459 DOI: 10.1038/s41467-022-28678-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 02/01/2022] [Indexed: 02/06/2023] Open
Abstract
Although recent work has described the microbiome in solid tumors, microbial content in hematological malignancies is not well-characterized. Here we analyze existing deep DNA sequence data from the blood and bone marrow of 1870 patients with myeloid malignancies, along with healthy controls, for bacterial, fungal, and viral content. After strict quality filtering, we find evidence for dysbiosis in disease cases, and distinct microbial signatures among disease subtypes. We also find that microbial content is associated with host gene mutations and with myeloblast cell percentages. In patients with low-risk myelodysplastic syndrome, we provide evidence that Epstein-Barr virus status refines risk stratification into more precise categories than the current standard. Motivated by these observations, we construct machine-learning classifiers that can discriminate among disease subtypes based solely on bacterial content. Our study highlights the association between the circulating microbiome and patient outcome, and its relationship with disease subtype.
Collapse
Affiliation(s)
- Jakob Woerner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Yidi Huang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | | | - Carmelo Gurnari
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | | | - Janet Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Yimin Huang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Daniel Schnabel
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Michael Aaby
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Wanying Xu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Vedant Thorat
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Dongxu Jiang
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | - Babal K Jha
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | - Mehmet Koyuturk
- Department of Computer Science, Case Western Reserve University, Cleveland, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | | | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA.
| |
Collapse
|
24
|
Metagenomic Sequencing Analysis for Acne Using Machine Learning Methods Adapted to Single or Multiple Data. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:8008731. [PMID: 34812271 PMCID: PMC8605909 DOI: 10.1155/2021/8008731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/24/2021] [Accepted: 10/05/2021] [Indexed: 11/17/2022]
Abstract
The human health status can be assessed by the means of research and analysis of the human microbiome. Acne is a common skin disease whose morbidity increases year by year. The lipids which influence acne to a large extent are studied by metagenomic methods in recent years. In this paper, machine learning methods are used to analyze metagenomic sequencing data of acne, i.e., all kinds of lipids in the face skin. Firstly, lipids data of the diseased skin (DS) samples and the healthy skin (HS) samples of acne patients and the normal control (NC) samples of healthy person are, respectively, analyzed by using principal component analysis (PCA) and kernel principal component analysis (KPCA). Then, the lipids which have main influence on each kind of sample are obtained. In addition, a multiset canonical correlation analysis (MCCA) is utilized to get lipids which can differentiate the face skins of the above three samples. The experimental results show the machine learning methods can effectively analyze metagenomic sequencing data of acne. According to the results, lipids which only influence one of the three samples or the lipids which simultaneously have different degree of influence on these three samples can be used as indicators to judge skin statuses.
Collapse
|
25
|
Jiang H, Wu C, Xu J, Wang Q, Shen L, Ou X, Liu H, Han X, Wang J, Ding W, Hu L, Chen X. Bacterial and Fungal Infections Promote the Bone Erosion Progression in Acquired Cholesteatoma Revealed by Metagenomic Next-Generation Sequencing. Front Microbiol 2021; 12:761111. [PMID: 34803987 PMCID: PMC8604023 DOI: 10.3389/fmicb.2021.761111] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/11/2021] [Indexed: 01/08/2023] Open
Abstract
An acquired cholesteatoma generally occurs as a consequence of otitis media and eustachian tube dysfunction. Patients with acquired cholesteatoma generally present with chronic otorrhea and progressive conductive hearing loss. There are many microbes reportedly associated with acquired cholesteatoma. However, conventional culture-based techniques show a typically low detection rate for various pathogenetic bacteria and fungi. Metagenomic next-generation sequencing (mNGS), an emerging powerful platform offering higher sensitivity and higher throughput for evaluating many samples at once, remains to be studied in acquired cholesteatoma. In this study, 16 consecutive patients from January 2020 to January 2021 at the Second Affiliated Hospital of Zhejiang University School of Medicine (SAHZU) were reviewed. We detected a total of 31 microbial species in patients, mNGS provided a higher detection rate compared to culture (100% vs. 31.25%, p = 0.000034). As the severity of the patient’s pathological condition worsens, the more complex types of microbes were identified. The most commonly detected microbial genus was Aspergillus (9/16, 56.25%), especially in patients suffering from severe bone erosion. In summary, mNGS improves the sensibility to identify pathogens of cholesteatoma patients, and Aspergillus infections increase bone destruction in acquired cholesteatoma.
Collapse
Affiliation(s)
- Hua Jiang
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengpeng Wu
- Eye Center of the Second Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingjie Xu
- Eye Center of the Second Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Wang
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lei Shen
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xunyan Ou
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongyan Liu
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xu Han
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Jun Wang
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Wenchao Ding
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Lidan Hu
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiangjun Chen
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Eye Center of the Second Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
26
|
Zhang T, Li H, Hou S, Yu H, Yue W. Case report of Ureaplasma urealyticum meningitis in a patient with thymoma and hypogammaglobulinaemia. BMC Infect Dis 2021; 21:1142. [PMID: 34749670 PMCID: PMC8573917 DOI: 10.1186/s12879-021-06831-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 10/22/2021] [Indexed: 11/10/2022] Open
Abstract
Background Ureaplasma urealyticum (UU) is found among the normal vaginal flora in a considerable proportion of asymptomatic women; however, adult central nervous system (CNS) infection of UU is extremely rare. Good's syndrome (GS) is an adult-onset immunodeficiency characterized by thymoma, hypogammaglobulinaemia, low or absent B‑cells, and an inverted CD4+/CD8+ T‑cell ratio. Patients with GS usually have severe or recurrent infections. Case presentation We describe the case report of a 49-year-old woman who developed UU meningitis. Initial routine anti-viral and anti-bacterial therapy showed no improvement in the patient's condition. Next-generation sequencing (NGS) of cerebrospinal fluid (CSF) identified the UU DNA sequence. Accordingly, a diagnosis of UU meningitis was made, and minocycline therapy was initiated. The patient responded favourably, with no signs of disease at subsequent follow-up. According to the severity and rarity of the case, secondary immunodeficiency was suspected. Flow cytometry found hypogammaglobulinaemia. Combined with the previous history of thymoma, the patient was diagnosed with immune deficiency disease of GS. Conclusions This case may be the first adult case report in the literature describing UU meningitis in a patient with GS. The diagnosis of GS should be considered in patients presenting with unexplained antibody deficiency and thymoma.
Collapse
Affiliation(s)
- Ting Zhang
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, China.,Department of Neurology, Tianjin Key Laboratory of Cerebrovascular and Neurodegenerative Diseases, Tianjin Huanhu Hospital, Tianjin, China
| | - Haiyan Li
- Department of Otolaryngology, Tianjin Key Laboratory of Cerebrovascular and Neurodegenerative Diseases, Tianjin Huanhu Hospital, Tianjin, China
| | - Shuping Hou
- Department of Dermatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Huanxin Yu
- Department of Otolaryngology, Tianjin Key Laboratory of Cerebrovascular and Neurodegenerative Diseases, Tianjin Huanhu Hospital, Tianjin, China
| | - Wei Yue
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical University, Tianjin, China. .,Department of Neurology, Tianjin Key Laboratory of Cerebrovascular and Neurodegenerative Diseases, Tianjin Huanhu Hospital, Tianjin, China.
| |
Collapse
|
27
|
Mahmoudi A, Kryštufek B, Sludsky A, Schmid BV, DE Almeida AMP, Lei X, Ramasindrazana B, Bertherat E, Yeszhanov A, Stenseth NC, Mostafavi E. Plague reservoir species throughout the world. Integr Zool 2021; 16:820-833. [PMID: 33264458 DOI: 10.1111/1749-4877.12511] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Plague has been known since ancient times as a re-emerging infectious disease, causing considerable socioeconomic burden in regional hotspots. To better understand the epidemiological cycle of the causative agent of the plague, its potential occurrence, and possible future dispersion, one must carefully consider the taxonomy, distribution, and ecological requirements of reservoir-species in relation either to natural or human-driven changes (e.g. climate change or urbanization). In recent years, the depth of knowledge on species taxonomy and species composition in different landscapes has undergone a dramatic expansion, driven by modern taxonomic methods such as synthetic surveys that take into consideration morphology, genetics, and the ecological setting of captured animals to establish their species identities. Here, we consider the recent taxonomic changes of the rodent species in known plague reservoirs and detail their distribution across the world, with a particular focus on those rodents considered to be keystone host species. A complete checklist of all known plague-infectable vertebrates living in plague foci is provided as a Supporting Information table.
Collapse
Affiliation(s)
- Ahmad Mahmoudi
- Department of Biology, Faculty of Science, Urmia University, Iran
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | | | - Alexander Sludsky
- Russian Research Anti-Plague Institute «Microbe», Saratov, Russian Federation
| | - Boris V Schmid
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Xu Lei
- State Key Laboratory of Integrated Management on Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Eric Bertherat
- Department of Infectious Hazard Management, Health Emergencies Programme, WHO, Geneva, Switzerland
| | - Aidyn Yeszhanov
- M.Aikimbaev's National Scientific Center for Especially Dangerous Infections, Almaty, Kazakhstan
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ehsan Mostafavi
- Department of Epidemiology and Biostatistics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
- National Reference Laboratory for Plague, Tularemia and Q fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
| |
Collapse
|
28
|
Piantadosi A, Mukerji SS, Ye S, Leone MJ, Freimark LM, Park D, Adams G, Lemieux J, Kanjilal S, Solomon IH, Ahmed AA, Goldstein R, Ganesh V, Ostrem B, Cummins KC, Thon JM, Kinsella CM, Rosenberg E, Frosch MP, Goldberg MB, Cho TA, Sabeti P. Enhanced Virus Detection and Metagenomic Sequencing in Patients with Meningitis and Encephalitis. mBio 2021; 12:e0114321. [PMID: 34465023 PMCID: PMC8406231 DOI: 10.1128/mbio.01143-21] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/02/2021] [Indexed: 01/21/2023] Open
Abstract
Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known (n = 44) or suspected (n = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. IMPORTANCE Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known (n = 44) or suspected (n = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections.
Collapse
Affiliation(s)
- Anne Piantadosi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Shibani S. Mukerji
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Simon Ye
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard-MIT Program of Health Sciences and Technology, Cambridge, Massachusetts, USA
| | - Michael J. Leone
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lisa M. Freimark
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daniel Park
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jacob Lemieux
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Sanjat Kanjilal
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Isaac H. Solomon
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Asim A. Ahmed
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Children’s Hospital, Boston, Massachusetts, USA
| | - Robert Goldstein
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Vijay Ganesh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Bridget Ostrem
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Kaelyn C. Cummins
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jesse M. Thon
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Cormac M. Kinsella
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Matthew P. Frosch
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marcia B. Goldberg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Tracey A. Cho
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- University of Iowa, Department of Neurology, Iowa City, Iowa, USA
| | - Pardis Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| |
Collapse
|
29
|
Chen F, Zhao Y, Shen C, Han L, Chen X, Zhang J, Xia Q, Qian Y. Next generation sequencing for diagnosis of central nervous system aspergillosis in liver transplant recipients. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1071. [PMID: 34422983 PMCID: PMC8339870 DOI: 10.21037/atm-21-92] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/08/2021] [Indexed: 01/19/2023]
Abstract
Background Fungal encephalitis is uncommon and sometimes fatal in liver transplant (LT) recipients. Early diagnosis of central nervous system (CNS) fungal infections, especially aspergillosis, is difficult based on routine tests of cerebrospinal fluid (CSF) alone. Next-generation sequencing (NGS) as a new tool may help in this respect. Methods Shotgun metagenomics was used to detect pathogens in CSF of patients, who were clinically suspected of CNS infection. Sequencing was performed at BGIseq-50 platform (BGI, Shenzhen). Results NGS technique identified Aspergillus in CSF of 5 patients, who were suspected of CNS infection, although clinical symptoms of these patients varied dramatically. The resulting sequence reads corresponding to Aspergillus species ranged from 2 to 25, with genomic coverage ranging from 0.0003% to 0.0036%. Rapid identification of Aspergillus enabled early appropriate antifungal therapy, although 4 patients eventually died of severe infection. Conclusions This is the first study to highlight the utility of NGS in early diagnosis of CNS aspergillosis in LT recipients. This new tool may be helpful in improving the diagnosis of CNS aspergillosis.
Collapse
Affiliation(s)
- Fang Chen
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China.,Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yujing Zhao
- Department of Anesthesiology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Chuan Shen
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Longzhi Han
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xiaosong Chen
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jianjun Zhang
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yongbing Qian
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| |
Collapse
|
30
|
Seronegative neurobrucellosis-do we need new neurobrucellosis criteria? Int J Infect Dis 2021; 111:124-126. [PMID: 34419580 DOI: 10.1016/j.ijid.2021.08.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/02/2021] [Accepted: 08/15/2021] [Indexed: 11/22/2022] Open
Abstract
Neurobrucellosis presents in various clinical forms and should always be considered in neurological patients in highly endemic areas such as the Mediterranean basin. Establishing a diagnosis can be challenging since serological testing can sometimes yield negative results. We present a rare case of a seronegative relapse of neurobrucellosis in a patient who had been successfully treated for systemic brucellosis. Oligoclonal bands, an agglutination test, and 16S rRNA sequencing of cerebrospinal fluid proved essential in unmasking a confined central nervous system relapse. This case reinforces the need for establishing diagnostic criteria for neurobrucellosis, which could potentially include oligoclonal bands and an agglutination test on the cerebrospinal fluid.
Collapse
|
31
|
Chen YH, Zheng HY, Li ZX, Wu YC, Niu ZX, Peng YH, Zhao JF, Sun Q. Distribution of bacteria infected by metagenomic sequencing technology in maxillofacial space. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2021; 39:475-481. [PMID: 34409806 PMCID: PMC8381121 DOI: 10.7518/hxkq.2021.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 03/05/2021] [Indexed: 01/23/2023]
Abstract
OBJECTIVES This study aimed to compare and analyze the consistency and difference between metageno-mic next-generation sequencing (mNGS) and conventional bacterial culture in the detection of pathogenic microorganisms in maxillofacial space infection, as well as to provide a new detection method for the early clinical identification of pathogenic bacteria in maxillofacial space infection. METHODS The clinical data of 16 patients with oral and maxillofacial space infections in the First Affiliated Hospital of Zhengzhou University from March 2020 to June 2020 were collected. mNGS and conventional bacterial culture methods were used to detect pus. We then analyzed and compared the test results of the two methods, including the test cycle, positive detection rate, anaerobic bacteria, facultative anaerobes and aerobic bacteria detection rates, distribution of pathogenic bacteria, relative species abundance, and resistance genes. RESULTS The average inspection period of mNGS was (18.81±3.73) h, and the average inspection period of bacterial culture was (83.25±11.64) h, the former was shorter than the latter (P<0.05). The positive detection rate of mNGS was 100% (16/16), and the positive detection rate of conventional bacterial culture was 31.25% (5/16), the former was higher than the latter (P<0.05). The detection rate of mNGS anaerobic bacteria was 93.75% (15/16), the detection rate of bacterial culture anaerobes was 0 (0/16), the former was higher than the latter (P<0.05). Using mNGS, the detection rate of facultative anaerobes in bacterial culture was 75.00% (12/16), and the detection rate of facultative anaerobes in bacterial culture was 25.00% (4/16), the former was higher than the latter (P<0.05). The detection rate of aerobic bacteria in bacterial culture was 12.50% (1/16), the former was higher than the latter (P>0.05). mNGS detected 15 kinds of pathogenic bacteria, among which 3 were Gram positive, 12 were Gram negative, 49 were non-pathogenic, 16 were Gram positive, and 32 were Gram negative, 1 was fungus. CONCLUSIONS Compared with conventional bacterial culture, mNGS has the characteristics of short test time, high sensitivity, and high accuracy. Thus, it is a new detection method for the early identification of pathogenic bacteria in maxillofacial space infection and is beneficial to the early clinical diagnosis and treatment of the disease.
Collapse
Affiliation(s)
- Yi-Heng Chen
- Dept. of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Hong-Yu Zheng
- Dept. of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zi-Xuan Li
- Dept. of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yong-Chao Wu
- Dept. of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhi-Xing Niu
- Dept. of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yan-Hui Peng
- Dept. of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jun-Fang Zhao
- Dept. of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Qiang Sun
- Dept. of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| |
Collapse
|
32
|
Chen B, Chen Z, Yang YS, Cai GL, Xu XJ, Guan HZ, Ren HT, Tuo HZ. Next-generation sequencing combined with serological tests based pathogen analysis for a neurocysticercosis patient with a 20-year history:a case report. BMC Neurol 2021; 21:236. [PMID: 34167488 PMCID: PMC8222500 DOI: 10.1186/s12883-021-02277-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/10/2021] [Indexed: 11/17/2022] Open
Abstract
Background Neurocysticercosis (NCC) is the most common helminthic infection of the central nervous system (CNS) caused by the larval stage of Taenia solium. Accurate and early diagnosis of NCC remains challenging due to its heterogeneous clinical manifestations, neuroimaging deficits, variable sensitivity, and specificity of serological tests. Next-generation sequencing (NGS)-based pathogen analysis in patient’s cerebrospinal fluid (CSF) with NCC infection has recently been reported indicating its diagnostic efficacy. In this case study, we report the diagnosis of a NCC patient with a symptomatic history of over 20 years using NGS analysis and further confirmation of the pathology by immunological tests. Case presentation This study reports the clinical imaging and immunological features of a patient with a recurrent headache for more than 20 years, which worsened gradually with the symptom of fever for more than 7 years and paroxysmal amaurosis for more than 1 year. By utilizing NGS technique, the pathogen was detected in patient’s CSF, and the presence of Taenia solium-DNA was confirmed by a positive immunological reaction to cysticercus IgG antibody in CSF and serum samples. The symptoms of the patient were alleviated, and the CSF condition was improved substantially after the anti-helminthic treatment. Conclusions This study suggests that combining CSF NGS with cysticercus IgG testing may be a highly promising approach for diagnosing the challenging cases of NCC. Further studies are needed to evaluate the parasitic DNA load in patients’ CSF for the diagnosis of disease severity, stage, and monitoring of therapeutic responses.
Collapse
Affiliation(s)
- Bin Chen
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zheng Chen
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yi-Shu Yang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Gui-Lan Cai
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xiao-Jiao Xu
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hong-Zhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hai-Tao Ren
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hou-Zhen Tuo
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China.
| |
Collapse
|
33
|
Khurana SK, Sehrawat A, Tiwari R, Prasad M, Gulati B, Shabbir MZ, Chhabra R, Karthik K, Patel SK, Pathak M, Iqbal Yatoo M, Gupta VK, Dhama K, Sah R, Chaicumpa W. Bovine brucellosis - a comprehensive review. Vet Q 2021; 41:61-88. [PMID: 33353489 PMCID: PMC7833053 DOI: 10.1080/01652176.2020.1868616] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Brucellosis is a zoonotic disease of great animal welfare and economic implications worldwide known since ancient times. The emergence of brucellosis in new areas as well as transmission of brucellosis from wild and domestic animals is of great significance in terms of new epidemiological dimensions. Brucellosis poses a major public health threat by the consumption of non-pasteurized milk and milk products produced by unhygienic dairy farms in endemic areas. Regular and meticulous surveillance is essentially required to determine the true picture of brucellosis especially in areas with continuous high prevalence. Additionally, international migration of humans, animals and trade of animal products has created a challenge for disease spread and diagnosis in non-endemic areas. Isolation and identification remain the gold standard test, which requires expertise. The advancement in diagnostic strategies coupled with screening of newly introduced animals is warranted to control the disease. Of note, the diagnostic value of miRNAs for appropriate detection of B. abortus infection has been shown. The most widely used vaccine strains to protect against Brucella infection and related abortions in cattle are strain 19 and RB51. Moreover, it is very important to note that no vaccine, which is highly protective, safe and effective is available either for bovines or human beings. Research results encourage the use of bacteriophage lysates in treatment of bovine brucellosis. One Health approach can aid in control of this disease, both in animals and man.
Collapse
Affiliation(s)
| | - Anju Sehrawat
- ICAR-Central Institute for Research on Buffaloes, Hisar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadyaya Pashu Chikitsa Vigyan Vishwavidyalya Evam Go-Anusandhan Sansthan (DUVASU), Mathura, Uttar Pradesh, India
| | - Minakshi Prasad
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences (LUVAS), Hisar, India
| | - Baldev Gulati
- ICAR-National Research Centre on Equine, Hisar, India
| | - Muhammad Zubair Shabbir
- Quality Operations Laboratory, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Rajesh Chhabra
- Department of Veterinary Microbiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences (LUVAS), Hisar, India
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamilnadu, India
| | - Shailesh Kumar Patel
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Mamta Pathak
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Mohd Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Vivek Kumar Gupta
- Centre for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| |
Collapse
|
34
|
Sung WH, Tsao YT, Shen CJ, Tsai CY, Cheng CM. Small-volume detection: platform developments for clinically-relevant applications. J Nanobiotechnology 2021; 19:114. [PMID: 33882955 PMCID: PMC8058587 DOI: 10.1186/s12951-021-00852-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022] Open
Abstract
Biochemical analysis of human body fluids is a frequent and fruitful strategy for disease diagnosis. Point-of-care (POC) diagnostics offers the tantalizing possibility of providing rapid diagnostic results in non-laboratory settings. Successful diagnostic testing using body fluids has been reported on in the literature; however, small-volume detection devices, which offer remarkable advantages such as portability, inexpensiveness, capacity for mass production, and tiny sample volume requirements have not been thoroughly discussed. Here, we review progress in this research field, with a focus on developments since 2015. In this review article, we provide a summary of articles that have detailed the development of small-volume detection strategies using clinical samples over the course of the last 5 years. Topics covered include small-volume detection strategies in ophthalmology, dermatology or plastic surgery, otolaryngology, and cerebrospinal fluid analysis. In ophthalmology, advances in technology could be applied to examine tear or anterior chamber (AC) fluid for glucose, lactoferrin, interferon, or VEGF. These approaches could impact detection and care for diseases including diabetic mellitus, dry-eye disease, and age-related maculopathy. Early detection and easy monitoring are critical approaches for improving overall care and outcome. In dermatology or plastic surgery, small-volume detection strategies have been applied for passive or interactive wound dressing, wound healing monitoring, and blister fluid analysis for autoimmune disease diagnosis. In otolaryngology, the analysis of nasal secretions and mucosa could be used to differentiate between allergic responses and infectious diseases. Cerebrospinal fluid analysis could be applied in neurodegenerative diseases, central neural system infection and tumor diagnosis. Other small-volume fluids that have been analyzed for diagnostic and monitoring purposes include semen and cervico-vaginal fluids. We include more details regarding each of these fluids, associated collection and detection devices, and approaches in our review.
Collapse
Affiliation(s)
- Wei-Hsuan Sung
- Chang Gung Memorial Hospital, Linkou Medical Center and Chang Gung Medical College and Chang Gung University, Taoyuan, Taiwan
| | - Yu-Ting Tsao
- Chang Gung Memorial Hospital, Linkou Medical Center and Chang Gung Medical College and Chang Gung University, Taoyuan, Taiwan
| | - Ching-Ju Shen
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chia-Ying Tsai
- Department of Ophthalmology, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City, Taiwan.
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan.
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, Taiwan.
| |
Collapse
|
35
|
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
|
36
|
Abstract
PURPOSE OF REVIEW Neurological conditions associated with HIV/AIDS including central nervous system (CNS), opportunistic infections (OI), chronic conditions including HIV-associated neurocognitive disorder, and cerebrospinal fluid (CSF) viral escape remain major contributors to morbidity and mortality worldwide. CNS infections in HIV-infected patients are often challenging to diagnose by traditional microbiological testing, impacting treatment and outcome. RECENT FINDINGS Recent advances in diagnostic techniques, including metagenomic next-generation sequencing (mNGS), are changing the landscape of microbiological testing, mainly in resource-rich settings. Pathogen discovery techniques offer a hypothesis-free approach to diagnostic testing, yielding comprehensive analysis of microbial genetic material. Given the extent of genetic material produced, deep sequencing tools not only hold promise in the diagnosis of CNS infections but also in defining key pathogenic steps which have previously been unanswered. Significant challenges remain to implementing pathogen discovery techniques in routine clinical practice including cost, expertise and infrastructure needed including laboratory and bioinformatics support, and sample contamination risk. The use in resource-limited regions where the burden of CNS complications due to HIV/AIDS is highest remains poorly defined. Though, major opportunities utilizing pathogen discovery techniques exist to enhance surveillance and diagnosis and improve our understanding of mechanisms of neuroinvasion in CNS conditions associated with HIV.
Collapse
Affiliation(s)
- Kiran T Thakur
- Columbia University Irving Medical Center, New York, NY, USA. .,New York Presbyterian Hospital, New York, NY, USA.
| |
Collapse
|
37
|
Duan H, Li X, Mei A, Li P, Liu Y, Li X, Li W, Wang C, Xie S. The diagnostic value of metagenomic next⁃generation sequencing in infectious diseases. BMC Infect Dis 2021; 21:62. [PMID: 33435894 PMCID: PMC7805029 DOI: 10.1186/s12879-020-05746-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 12/27/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although traditional diagnostic techniques of infection are mature and price favorable at present, most of them are time-consuming and with a low positivity. Metagenomic next⁃generation sequencing (mNGS) was studied widely because of identification and typing of all pathogens not rely on culture and retrieving all DNA without bias. Based on this background, we aim to detect the difference between mNGS and traditional culture method, and to explore the relationship between mNGS results and the severity, prognosis of infectious patients. METHODS 109 adult patients were enrolled in our study in Shanghai Tenth People's Hospital from October 2018 to December 2019. The diagnostic results, negative predictive values, positive predictive values, false positive rate, false negative rate, pathogen and sample types were analyzed by using both traditional culture and mNGS methods. Then, the samples and clinical information of 93 patients in the infected group (ID) were collected. According to whether mNGS detected pathogens, the patients in ID group were divided into the positive group of 67 cases and the negative group of 26 cases. Peripheral blood leukocytes, C-reactive protein (CRP), procalcitonin (PCT) and neutrophil counts were measured, and the concentrations of IL-2, IL-4, IL-6, TNF-α, IL-17A, IL-10 and INF-γ in the serum were determined by ELISA. The correlation between the positive detection of pathogens by mNGS and the severity of illness, hospitalization days, and mortality were analyzed. RESULTS 109 samples were assigned into infected group (ID, 92/109, 84.4%), non-infected group (NID, 16/109, 14.7%), and unknown group (1/109, 0.9%). Blood was the most abundant type of samples with 37 cases, followed by bronchoalveolar lavage fluid in 36 cases, tissue, sputum, pleural effusion, cerebrospinal fluid (CSF), pus, bone marrow and nasal swab. In the ID group, the majority of patients were diagnosed with lower respiratory system infections (73/109, 67%), followed by bloodstream infections, pleural effusion and central nervous system infections. The sensitivity of mNGS was significantly higher than that of culture method (67.4% vs 23.6%; P < 0.001), especially in sample types of bronchoalveolar lavage fluid (P = 0.002), blood (P < 0.001) and sputum (P = 0.037), while the specificity of mNGS was not significantly different from culture method (68.8% vs 81.3%; P = 0.41). The number of hospitals stays and 28-day-motality in the positive mNGS group were significantly higher than those in the negative group, and the difference was statistically significant (P < 0.05). Age was significant in multivariate logistic analyses of positive results of mNGS. CONCLUSIONS The study found that mNGS had a higher sensitivity than the traditional method, especially in blood, bronchoalveolar lavage fluid and sputum samples. And positive mNGS group had a higher hospital stay, 28-day-mortality, which means the positive of pathogen nucleic acid sequences detection may be a potential high-risk factor for poor prognosis of adult patients and has significant clinical value. MNGS should be used more in early pathogen diagnosis in the future.
Collapse
Affiliation(s)
- Hongxia Duan
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, #301, Mid Yanchang Rd, Shanghai, 200072, China
| | - Xuan Li
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, #301, Mid Yanchang Rd, Shanghai, 200072, China
| | - Aihong Mei
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, #301, Mid Yanchang Rd, Shanghai, 200072, China
| | - Ping Li
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, #301, Mid Yanchang Rd, Shanghai, 200072, China
| | - Yang Liu
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, #301, Mid Yanchang Rd, Shanghai, 200072, China
| | - Xiaofeng Li
- Department of Emergency, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Weiwei Li
- Department of Geriatrics, Shanghai 10th People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Changhui Wang
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, #301, Mid Yanchang Rd, Shanghai, 200072, China.
| | - Shuanshuan Xie
- Department of Respiratory Medicine, Shanghai 10th People's Hospital, Tongji University School of Medicine, #301, Mid Yanchang Rd, Shanghai, 200072, China.
| |
Collapse
|
38
|
Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
Collapse
Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| |
Collapse
|
39
|
Abstract
Brucellosis is a common Zoonosis affecting half a million people annually. The most common mode of infection is by consuming unpasteurized milk or milk products. The general manifestations are those of fever with generalized symptoms. The nervous system is affected in 4-7% of cases. The manifestations are protean and include meningo-encephalitis as well as peripheral nervous system involvement. The diagnosis relies on culture, which is cumbersome and can be falsely negative. Agglutination tests for the various species of the organism are the mainstay for diagnosis. Treatment is for 3-6 months with combination therapy including Doxycycline, Rifampicin and ceftriaxone. The main issue is prevention and better animal husbandry.
Collapse
Affiliation(s)
- Raad Shakir
- Division of Brain Sciences, Imperial College, London, UK.
| |
Collapse
|
40
|
Fan S, Xiao M, Han F, Xia P, Bai X, Chen H, Zhang H, Ding X, Zhao H, Zhao J, Sun X, Jiang W, Wang C, Cao W, Guo F, Tian R, Gao P, Wu W, Ma J, Wu D, Liu Z, Zhou X, Wang J, Guan T, Qin Y, Li T, Xu Y, Zhang D, Chen Y, Xie J, Li Y, Yan X, Zhu Y, Peng B, Cui L, Zhang S, Guan H. Neurological Manifestations in Critically Ill Patients With COVID-19: A Retrospective Study. Front Neurol 2020; 11:806. [PMID: 32754114 PMCID: PMC7365850 DOI: 10.3389/fneur.2020.00806] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023] Open
Abstract
Background: The complications of coronavirus disease 2019 (COVID-19) involved multiple organs or systems, especially in critically ill patients. We aim to investigate the neurological complications in critically ill patients with COVID-19. Methods: This retrospective single-center case series analyzed critically ill patients with COVID-19 at the intensive care unit of Tongji Hospital, Wuhan, China from February 5 to April 2, 2020. Demographic data, clinical and laboratory findings, comorbidities and treatments were collected and analyzed. Results: Among 86 patients with confirmed COVID-19, 54 patients (62.8%) were male, and the mean (SD) age was 66.6 (11.1) years. Overall, 65% patients presented with at least one neurological symptom. Twenty patients (23.3%) had symptoms involving the central nervous system, including delirium, cerebrovascular diseases and hypoxic-ischemic brain injury, while 6 patients (7%) had neuromuscular involvement. Seven of 86 patients exhibited new stroke and 6 (7%) cases were ischemic. A significantly higher prevalence of antiphospholipid antibodies was observed in patients with ischemic stroke than in those without stroke (83.3 vs. 26.9%, p < 0.05). Patients with ischemic stroke were more likely to have a higher myoglobulin level, and a lower hemoglobin level. Conclusions: The clinical spectrum of neurological complications in critically ill patients with COVID-19 was broad. Stroke, delirium and neuromuscular diseases are common neurological complications of COVID-19. Physicians should pay close attention to neurological complications in critically ill patients with COVID-19.
Collapse
Affiliation(s)
- Siyuan Fan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Han
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Peng Xia
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyin Bai
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Huan Chen
- Department of Intensive Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongmin Zhang
- Department of Intensive Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Ding
- Department of Intensive Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Hua Zhao
- Department of Intensive Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing Zhao
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuefeng Sun
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Jiang
- Department of Medical Intensive Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Chunyao Wang
- Department of Medical Intensive Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Cao
- Department of Infectious Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Fan Guo
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ran Tian
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Peng Gao
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Wu
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jie Ma
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Wu
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhengyin Liu
- Department of Infectious Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiang Zhou
- Department of Intensive Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jinglan Wang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Tianjia Guan
- School of Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Qin
- Department of Nephrology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Taisheng Li
- Department of Infectious Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Chen
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing Xie
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yongzhe Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaowei Yan
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yicheng Zhu
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Peng
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongzhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| |
Collapse
|
41
|
Fan S, Yuan H, Liu L, Li H, Wang S, Zhao W, Wu Y, Wang P, Hu Y, Han J, Lyu Y, Zhang W, Chen P, Wu H, Gong Y, Ma Z, Li Y, Yu J, Qiao X, Li G, Zhao Y, Wang D, Ren H, Peng B, Cui L, Wang J, Guan H. Pseudorabies virus encephalitis in humans: a case series study. J Neurovirol 2020; 26:556-564. [PMID: 32572833 DOI: 10.1007/s13365-020-00855-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 03/21/2020] [Accepted: 05/14/2020] [Indexed: 12/13/2022]
Abstract
Pseudorabies virus (PRV) is known to cause severe encephalitis in juvenile pigs and various non-native hosts; recent evidences suggest that PRV might cause encephalitis in humans. In a multicenter cohort study in China, next-generation sequencing of cerebrospinal fluid (CSF) was performed to detect pathogens in all patients with clinically suspected central nervous system infections. This study involved all the patients whose CSF samples were positive for PRV-DNA; their clinical features were evaluated, and species-specific PCR and serological tests were sequentially applied for validation. Among the 472 patients tested from June 1, 2016, to December 1, 2018, six were positive for PRV-DNA, which were partially validated by PCR and serological tests. Additionally, we retrospectively examined another case with similar clinical and neuroimaging appearance and detected the presence of PRV-DNA. These patients had similar clinical manifestations, including a rapid progression of panencephalitis, and similar neuroimaging features of symmetric lesions in the basal ganglia and bilateral hemispheres. Six of the patients were engaged in occupations connected with swine production. PRV infection should be suspected in patients with rapidly progressive panencephalitis and characteristic neuroimaging features, especially with exposure to swine.
Collapse
MESH Headings
- Adult
- Animals
- Antibodies, Viral/cerebrospinal fluid
- Basal Ganglia/diagnostic imaging
- Basal Ganglia/pathology
- Basal Ganglia/virology
- Cerebrum/diagnostic imaging
- Cerebrum/pathology
- Cerebrum/virology
- China
- DNA, Viral/cerebrospinal fluid
- DNA, Viral/genetics
- Encephalitis, Viral/cerebrospinal fluid
- Encephalitis, Viral/diagnosis
- Encephalitis, Viral/pathology
- Encephalitis, Viral/virology
- Female
- Herpesvirus 1, Suid/genetics
- Herpesvirus 1, Suid/growth & development
- Herpesvirus 1, Suid/pathogenicity
- High-Throughput Nucleotide Sequencing
- Humans
- Magnetic Resonance Imaging
- Male
- Meat/virology
- Middle Aged
- Polymerase Chain Reaction
- Pseudorabies/cerebrospinal fluid
- Pseudorabies/diagnosis
- Pseudorabies/pathology
- Pseudorabies/virology
- Swine
Collapse
Affiliation(s)
- Siyuan Fan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Hongxun Yuan
- Department of Intensive Care Unit, Peking University International Hospital, Beijing, China
| | - Lei Liu
- Department of Neurology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Hongfang Li
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, China
| | - Shengnan Wang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Weili Zhao
- Department of Neurology, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Yihan Wu
- Department of Neurology, Inner Mongolia People's Hospital, Hohhot, China
| | - Pei Wang
- Department of Neurology, Baoding No.1 Central Hospital, Baoding, China
| | - Yafang Hu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yanli Lyu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wuchao Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Peng Chen
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Honglong Wu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Yanping Gong
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhenzi Ma
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Yongjun Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - JiaoJiao Yu
- Department of Intensive Care Unit, Peking University International Hospital, Beijing, China
| | - Xiaodong Qiao
- Department of Neurology, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Guoli Li
- Department of Neurology, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Yan Zhao
- Department of Neurology, Inner Mongolia People's Hospital, Hohhot, China
| | - Dexin Wang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Haitao Ren
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Bin Peng
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jiawei Wang
- Department of Neurology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
| | - Hongzhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| |
Collapse
|
42
|
Zou Y, Guan H, Wu H, Bu H, Yan L, Zhu Y, He J. Angiostrongyliasis detected by next-generation sequencing in a ELISA-negative eosinophilic meningitis: A case report. Int J Infect Dis 2020; 97:177-179. [PMID: 32502661 DOI: 10.1016/j.ijid.2020.05.108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 10/24/2022] Open
Abstract
Next-generation sequencing (NGS) is an emerging method with the potential of pan-pathogen screening. This study described a case of eosinophilic meningitis (EoM) with enzyme-linked immunosorbent assay (ELISA)-negative results for Angiostrongylus cantonensis (A. cantonensis), Trichinella spiralis and Paragonimus westermani and a positive identification of A. cantonensis by NGS in the cerebrospinal fluid.
Collapse
Affiliation(s)
- Yueli Zou
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hongzhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Honglong Wu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Hui Bu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Litian Yan
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yifei Zhu
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
| | - Junying He
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
| |
Collapse
|
43
|
Fei X, Li C, Zhang Y, Zhang H, Liu X, Ji X, Shi Y, Liu N, Wu M, Du F, Yang Y, Dai W, Liu T, He Y, Bian T, Zhou H, An X, Cai Z, Shi J, Feng G, Shi M, Zhao G. Next-generation sequencing of cerebrospinal fluid for the diagnosis of neurocysticercosis. Clin Neurol Neurosurg 2020; 193:105752. [PMID: 32220712 DOI: 10.1016/j.clineuro.2020.105752] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/10/2020] [Accepted: 02/25/2020] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Neurocysticercosis (NCC) is the most common parasitic disease of the human central nervous system (CNS). However, a diagnosis of NCC may be hard to make if the specific clinical and routine neuroimaging manifestations are lacking, which hinders physicians from considering further immunodiagnostic tests. PATIENTS AND METHODS Seven patients presented with fever, headache, nausea, cognitive decline, confusion, or progressive leg weakness. There were no pathogens found in the cerebrospinal fluid (CSF); patients were clinically suspected of meningoencephalitis or cerebrovascular disease. To clearly determine the etiology, next generation sequencing (NGS) of the CSF was used to detect pathogens in these seven patients. RESULTS Taenia solium DNA sequences were detected in the seven patients, but not in the non-template controls (NTCs) or the other patients with clinically suspected CNS infections. Based on the patients' medical data and the diagnostic criteria for NCC, seven patients were diagnosed with probable NCC. The unique reads aligning to Taenia solium ranged from 6 to 261064, with genomic coverage ranging from 0.0003% to 14.8079%. The number of unique reads and genomic coverage dropped in three of the seven patients after antiparasitic treatment, consistent with the relief of symptoms. CONCLUSION This study showed that NGS of the CSF might be an auxiliary diagnostic method for NCC patients. Larger studies are required.
Collapse
Affiliation(s)
- Xiaofei Fei
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Chaoyang Li
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Yun Zhang
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Hongya Zhang
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Xuewu Liu
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Xinchao Ji
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Yajun Shi
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Na Liu
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Mengli Wu
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Fang Du
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Yining Yang
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Wen Dai
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - TingTing Liu
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Ying He
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Ting Bian
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Huimin Zhou
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Xingyue An
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Zheng Cai
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China
| | - Jian Shi
- Department of Neurology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang, Henan, China
| | - Guodong Feng
- Department of Neurology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
| | - Ming Shi
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China.
| | - Gang Zhao
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, 15 Changle xi Road, Xi'an, 710032, China.
| |
Collapse
|
44
|
Dai Y, Chen L, Chang W, Lu H, Cui P, Ma X. Culture-Negative Streptococcus suis Infection Diagnosed by Metagenomic Next-Generation Sequencing. Front Public Health 2019; 7:379. [PMID: 31921744 PMCID: PMC6928000 DOI: 10.3389/fpubh.2019.00379] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/26/2019] [Indexed: 12/02/2022] Open
Abstract
Background:Streptococcus suis is a zoonotic pathogen that can cause severe infections such as meningitis and septicemia in both swine and humans. Rapid and accurate identification of the causative agent is very important for guiding clinical choices in administering countermeasures. Case Report: Here, we report a case of fatal S. suis infection in a patient who worked as a butcher in China. The 59-year-old man, who had previously undergone splenectomy, injured his finger while processing pork and developed severe sepsis. While blood cultures were negative following antibiotic treatment, S. suis was determined to be the causative agent by metagenomic next-generation sequencing (mNGS) and Sanger sequencing. Conclusion: Identification of etiological agents using techniques such as blood culture prior to antibiotic treatment is very important. mNGS may represent a useful method for diagnosis of infectious diseases, especially post-antibiotic treatment.
Collapse
Affiliation(s)
- Yuanyuan Dai
- Department of Clinical Laboratory, First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Li Chen
- Department of Clinical Laboratory, First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Wenjiao Chang
- Department of Clinical Laboratory, First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Huaiwei Lu
- Department of Clinical Laboratory, First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Peng Cui
- Infectious Disease Research and Development, Beijing Genomics Institute-Shanghai, Shanghai, China
| | - Xiaoling Ma
- Department of Clinical Laboratory, First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| |
Collapse
|
45
|
Han D, Li Z, Li R, Tan P, Zhang R, Li J. mNGS in clinical microbiology laboratories: on the road to maturity. Crit Rev Microbiol 2019; 45:668-685. [PMID: 31691607 DOI: 10.1080/1040841x.2019.1681933] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical laboratories for unbiased culture-independent diagnosis. Whether it can be a next routine pathogen identification tool has become a topic of concern. We review the current implementation of this new technology for infectious disease diagnostics and discuss the feasibility of transforming mNGS into a routine diagnostic test. Since 2008, numerous studies from over 20 countries have revealed the practicality of mNGS in the work-up of undiagnosed infectious diseases. mNGS performs well in identifying rare, novel, difficult-to-detect and coinfected pathogens directly from clinical samples and presents great potential in resistance prediction by sequencing the antibiotic resistance genes, providing new diagnostic evidence that can be used to guide treatment options and improve antibiotic stewardship. Many physicians recognized mNGS as a last resort method to address clinical infection problems. Although several hurdles, such as workflow validation, quality control, method standardisation, and data interpretation, remain before mNGS can be implemented routinely in clinical laboratories, they are temporary and can be overcome by rapidly evolving technologies. With more validated workflows, lower cost and turnaround time, and simplified interpretation criteria, mNGS will be widely accepted in clinical practice. Overall, mNGS is transforming the landscape of clinical microbiology laboratories, and to ensure that it is properly utilised in clinical diagnosis, both physicians and microbiologists should have a thorough understanding of the power and limitations of this method.
Collapse
Affiliation(s)
- Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ziyang Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| |
Collapse
|
46
|
Huang Y, Ma Y, Miao Q, Pan J, Hu B, Gong Y, Lin Y. Arthritis caused by Legionella micdadei and Staphylococcus aureus: metagenomic next-generation sequencing provides a rapid and accurate access to diagnosis and surveillance. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:589. [PMID: 31807570 DOI: 10.21037/atm.2019.09.81] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Legionella spp. is an important pulmonary pathogen but rarely causes extra-pulmonary infections. We report a case of joint infection caused by Legionella micdadei and Staphylococcus aureus in a 54-year-old male with medication history of oral steroid for systemic lupus erythematosus (SLE). He developed arthritis in his right metacarpophalangeal (MCP) joints without precursor pneumonia. In the joint aspirate, S. aureus was detected through culture. The existence of L. micdadei and S. aureus were indicated by metagenomic next-generation sequencing (mNGS) and confirmed by 16S rRNA sequence analysis. After oral levofloxacin treatment for 54 days, the patient's symptoms ameliorated and blood test results improved, which were consistent with the dynamic trend of reads numbers in mNGS data. Our case included, arthritis caused by Legionella spp. have been reported in 11 patients. However, our case is the first to report septic arthritis caused by L. micdadei in native joints and monitored by mNGS. This case demonstrated an application of mNGS for etiological diagnosis and semi-quantification in joint aspirate. mNGS may serve as a promising tool for rapid and accurate etiological diagnosis and surveillance, contributing to appropriate antimicrobial drug applications and timely medication adjustments when necessary.
Collapse
Affiliation(s)
- Yingnan Huang
- Department of infectious diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yuyan Ma
- Department of infectious diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qing Miao
- Department of infectious diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jue Pan
- Department of infectious diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Bijie Hu
- Department of infectious diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yanping Gong
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Yang Lin
- Wuhan research and development of infectious diseases department, BGI-Wuhan, Wuhan 430075, China
| |
Collapse
|
47
|
Wang S, Chen Y, Wang D, Wu Y, Zhao D, Zhang J, Xie H, Gong Y, Sun R, Nie X, Jiang H, Zhang J, Li W, Liu G, Li X, Huang K, Huang Y, Li Y, Guan H, Pan S, Hu Y. The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid. Front Microbiol 2019; 10:1993. [PMID: 31551954 PMCID: PMC6733977 DOI: 10.3389/fmicb.2019.01993] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 08/14/2019] [Indexed: 01/22/2023] Open
Abstract
Purpose The application of metagenomic next-generation sequencing (mNGS) in the diagnosis of tuberculous meningitis (TBM) remains poorly characterized. Here, we retrospectively analyzed data from patients with TBM who had taken both mNGS and conventional tests including culture of Mycobacterium tuberculosis (MTB), polymerase chain reaction (PCR) and acid-fast bacillus (AFB) stain, and the sensitivity and specificity of these methods were compared. Methods We retrospectively recruited TBM patients admitted to the hospital between December 2015 and October 2018. The first collection of cerebrospinal fluid (CSF) samples underwent both mNGS and conventional tests. In addition, patients with bacterial/cryptococcal meningitis or viral meningoencephalitis were mNGS positive controls, and a patient with auto-immune encephalitis was an mNGS negative control. Results Twenty three TBM patients were classified as 12 definite and 11 clinical diagnoses, which were based on clinical manifestations, pathogen evidence, CSF parameters, brain imaging, and treatment response. The mNGS method identified sequences of Mycobacterium tuberculosis complex (MBTC) from 18 samples (18/23, 78.26%). In patients with definite TBM, the sensitivity of mNGS, AFB, PCR, and culture to detect MTB in the first CSF samples were 66.67, 33.33, 25, and 8.33%, respectively. The specificity of each method was 100%. Among the four negative mNGS cases (4/23, 17.39%), three turned out positive by repeated AFB stain. The agreement of mNGS with the total of conventional methods was 44.44% (8/18). Combination of mNGS and conventional methods increased the detection rate to 95.65%. One patient was diagnosed as complex of TBM and cryptococcal meningitis, in which AFB stain and cryptococcal antigen enzyme immunoassay were positive and the DNA of Cryptococcus neoformans was detected by mNGS. Conclusion Our study indicates that mNGS is an alternative method to detect the presence of mycobacterial DNA in CSF samples from patients with TBM and deserves to be applied as a front-line CSF test.
Collapse
Affiliation(s)
- Shengnan Wang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yingli Chen
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dongmei Wang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongming Wu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Deqiang Zhao
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jianzhao Zhang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Huifang Xie
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yanping Gong
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Ruixue Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Xifang Nie
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Haishan Jiang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wei Li
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guanghui Liu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuan Li
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kaibin Huang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yingwei Huang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongjun Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hongzhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Suyue Pan
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yafang Hu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
48
|
Abstract
Patients with central nervous system (CNS) infection experience very high levels of morbidity and mortality, in part because of the many challenges inherent to the diagnosis of CNS infection and identification of a causative pathogen. The clinical presentation of CNS infection is nonspecific, so clinicians must often order and interpret many diagnostic tests in parallel. This can be a daunting task given the large number of potential pathogens and the availability of different testing modalities. Here, we review traditional diagnostic techniques including Gram stain and culture, serology, and polymerase chain reaction (PCR). We highlight which of these are recommended for the pathogens most commonly tested among U.S. patients with suspected CNS infection. Finally, we describe the newer broad-range diagnostic approaches, multiplex PCR and metagenomic sequencing, which are increasingly used in clinical practice.
Collapse
Affiliation(s)
- Sanjat Kanjilal
- Division of Infectious Diseases, Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts
| | - Tracey A Cho
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Anne Piantadosi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts
| |
Collapse
|
49
|
Zhang XX, Guo LY, Liu LL, Shen A, Feng WY, Huang WH, Hu HL, Hu B, Guo X, Chen TM, Chen HY, Jiang YQ, Liu G. The diagnostic value of metagenomic next-generation sequencing for identifying Streptococcus pneumoniae in paediatric bacterial meningitis. BMC Infect Dis 2019; 19:495. [PMID: 31164085 PMCID: PMC6549306 DOI: 10.1186/s12879-019-4132-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/24/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND There is currently no research on the diagnostic value of metagenomic next-generation sequencing (mNGS) for a single pathogens in CSF. The aim of this study was to analyse the value of mNGS for identifying Streptococcus pneumoniae (S. pneumoniae) in paediatric bacterial meningitis. METHODS Bacterial meningitis (BM) cases from October 23, 2014, to December 31, 2016, and December 1, 2017, to July 31, 2018 at Beijing Children's Hospital were reviewed. Clinical features and pathogens were analysed. RESULTS We diagnosed 135 patients with BM in this study. A total of 43 S. pneumoniae were identified by combination methods. 26/135 (19.3%) patients had positive results in S. pneumoniae by blood and/or cerebrospinal fluid (CSF) culture. Alere BinaxNow®Streptococcus pneumoniae Antigen test was positive in 35/135(25.9%) cases. 32/135 (23.7%) S. pneumoniae were identified by mNGS. Six CSF samples were identified as S. pneumoniae only by mNGS technology. Taking culture as the gold standard, the sensitivity and specificity of mNGS for diagnosing S. pneumoniae meningitis were 73.1 and 88.1%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) of diagnosing S. pneumoniae meningitis by mNGS were 59.4 and 93.2%, respectively. When comparison between mNGS and combined tests (culture and Alere BinaxNow®Streptococcus pneumoniae Antigen test), the sensitivity and specificity of mNGS for S. pneumoniae identification were 70.3 and 93.9%, the PPV and NPV in the identification of S. pneumoniae by mNGS were 81.4 and 89.3%, respectively. The difference in number of unique reads of S. pneumoniaein from CSF sample (< 14 days onset) and CSF sample (> 14 days from onset) was statistically significant (170.5 VS. 13, P = 0.019). The difference in the collected time of CSF for culture and mNGS was statistically significant (4 days VS. 14 days, P < 0.001). CONCLUSIONS mNGS has high sensitivity and specificity for S. pneumoniae identification. The pathogen load (number of unique reads) of S. pneumonia is related to the CSF collection time. mNGS was less affected than culture by the use of antibiotics before CSF collection.
Collapse
MESH Headings
- Adolescent
- Age Factors
- Antigens, Bacterial/analysis
- Antigens, Bacterial/blood
- Antigens, Bacterial/cerebrospinal fluid
- Antigens, Bacterial/genetics
- Child
- Child, Preschool
- Diagnostic Tests, Routine
- Female
- High-Throughput Nucleotide Sequencing
- Humans
- Infant
- Infant, Newborn
- Male
- Meningitis, Bacterial/blood
- Meningitis, Bacterial/cerebrospinal fluid
- Meningitis, Bacterial/diagnosis
- Meningitis, Bacterial/microbiology
- Metagenomics/methods
- Pediatrics/methods
- Polymerase Chain Reaction/methods
- Predictive Value of Tests
- Sensitivity and Specificity
- Streptococcus pneumoniae/genetics
- Streptococcus pneumoniae/isolation & purification
Collapse
Affiliation(s)
- Xi-Xi Zhang
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Ling-Yun Guo
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Lin-Lin Liu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Ao Shen
- Tianjin Medical Laboratory, BGI-Tianjin, Tianjin, China
| | - Wen-Ya Feng
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Wen-Hua Huang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, 100071, China
| | - Hui-Li Hu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Bing Hu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Xin Guo
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Tian-Ming Chen
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - He-Ying Chen
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China
| | - Yong-Qiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, 100071, China
| | - Gang Liu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56 Nan Lishi Road, Beijing, 100045, China.
| |
Collapse
|
50
|
Xiao W, Han P, Xu Z, Huang M. Pulmonary scedosporiosis in a patient with acute hematopoietic failure: Diagnosis aided by next-generation sequencing. Int J Infect Dis 2019; 85:114-116. [PMID: 31170547 DOI: 10.1016/j.ijid.2019.05.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/15/2019] [Accepted: 05/25/2019] [Indexed: 10/26/2022] Open
Abstract
We report the first case of pulmonary scedosporiosis detected by next-generation sequencing (NGS) from bronchoalveolar lavage fluid (BALF) in a 67-year-old male with bronchiectasis and hematopoietic failure. Scedosporium apiospermum is a ubiquitous organism present in the environment with intrinsic resistance to many antifungal agents. The patient developed respiratory failure, pulmonary consolidation, and septic shock shortly thereafter, and responded poorly to antifungal therapy. This case highlights the combined application of NGS and traditional fungal culture in the clinical diagnosis of pulmonary invasive fungal disease. NGS is proposed as an important adjunctive diagnostic approach for uncommon pathogens.
Collapse
Affiliation(s)
- Wei Xiao
- Department of General Intensive Care Unit, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Pan Han
- Department of General Intensive Care Unit, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhijun Xu
- Department of General Intensive Care Unit, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Man Huang
- Department of General Intensive Care Unit, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| |
Collapse
|