1
|
Makkawi S, Alqurashi S, Hubayni W, Almahdawi S, Bahkali S, Alharbi A, Khojah O, Halawani A, Malli I. The Clinical Manifestations, Risk Factors, Etiologies, and Outcomes of Adult Patients with Infectious Meningitis and Encephalitis: Single Center Experience. Neurol Int 2024; 16:966-975. [PMID: 39311346 PMCID: PMC11417761 DOI: 10.3390/neurolint16050073] [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: 06/19/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/26/2024] Open
Abstract
(1) Background: Central nervous system (CNS) infections, including meningitis and encephalitis, are serious conditions which are associated with high morbidity and mortality. This study aims to identify the clinical manifestations, etiologies, and outcomes of meningitis and encephalitis in adult patients in Saudi Arabia, addressing the current gap in understanding these conditions within this population. (2) Methods: This is a single-center retrospective study which included all adult patients diagnosed with meningitis and encephalitis from March 2016 to May 2022. (3) Results: This study found that most cases of meningitis and encephalitis occurred due to unknown pathogens. Pretreatment with antibiotics prior to lumbar puncture (LP) was found in 71.2% of patients with meningitis. Altered mental status and seizures were common presenting symptoms among patients with encephalitis while altered mental status and fever were common among patients with meningitis. (4) Conclusions: Adherence to guidelines in treating meningitis and encephalitis and performing LPs in a timely manner are important. Establishing national biobanks with biological samples from patients suspected of having meningitis or encephalitis will significantly enhance our understanding of these conditions in Saudi Arabia.
Collapse
Affiliation(s)
- Seraj Makkawi
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah 22384, Saudi Arabia (W.H.)
- King Abdullah International Medical Research Center, Jeddah 22384, Saudi Arabia;
- Department of Neuroscience, Ministry of the National Guard-Health Affairs, Jeddah 22384, Saudi Arabia
| | - Shatha Alqurashi
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah 22384, Saudi Arabia (W.H.)
| | - Wejdan Hubayni
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah 22384, Saudi Arabia (W.H.)
| | - Saleha Almahdawi
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah 22384, Saudi Arabia (W.H.)
| | - Sadeem Bahkali
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah 22384, Saudi Arabia (W.H.)
| | - Abeer Alharbi
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah 22384, Saudi Arabia (W.H.)
| | - Osama Khojah
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah 22384, Saudi Arabia (W.H.)
- King Abdullah International Medical Research Center, Jeddah 22384, Saudi Arabia;
- Department of Neuroscience, Ministry of the National Guard-Health Affairs, Jeddah 22384, Saudi Arabia
| | - Aisha Halawani
- King Abdullah International Medical Research Center, Jeddah 22384, Saudi Arabia;
- Department of Medical Imaging, Ministry of the National Guard-Health Affairs, Jeddah 22384, Saudi Arabia
| | - Israa Malli
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah 22384, Saudi Arabia (W.H.)
- King Abdullah International Medical Research Center, Jeddah 22384, Saudi Arabia;
| |
Collapse
|
2
|
Cao H, Chen Y, Ge L, Kwong JSW, Lai H, Hu F, Zhang R, Zhao H, Hu L, He R, Zheng W, Zhang J. An umbrella review of the diagnostic value of next-generation sequencing in infectious diseases. Int J Clin Pharm 2024; 46:780-794. [PMID: 38570474 DOI: 10.1007/s11096-024-01704-2] [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: 12/15/2023] [Accepted: 01/18/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND An increasing number of systematic reviews (SRs) have evaluated the diagnostic values of next-generation sequencing (NGS) in infectious diseases (IDs). AIM This umbrella analysis aimed to assess the potential risk of bias in existing SRs and to summarize the published diagnostic values of NGS in different IDs. METHOD We searched PubMed, Embase, and the Cochrane Library until September 2023 for SRs assessing the diagnostic validity of NGS for IDs. Two investigators independently determined review eligibility, extracted data, and evaluated reporting quality, risk of bias, methodological quality, and evidence certainty in the included SRs. RESULTS Eleven SRs were analyzed. Most SRs exhibited a moderate level of reporting quality, while a serious risk of bias was observed in all SRs. The diagnostic performance of NGS in detecting pneumocystis pneumonia and periprosthetic/prosthetic joint infection was notably robust, showing excellent sensitivity (pneumocystis pneumonia: 0.96, 95% CI 0.90-0.99, very low certainty; periprosthetic/prosthetic joint infection: 0.93, 95% CI 0.83-0.97, very low certainty) and specificity (pneumocystis pneumonia: 0.96, 95% CI 0.92-0.98, very low certainty; periprosthetic/prosthetic joint infection: 0.95, 95% CI 0.92-0.97, very low certainty). NGS exhibited high specificity for central nervous system infection, bacterial meningoencephalitis, and tuberculous meningitis. The sensitivity to these infectious diseases was moderate. NGS demonstrated moderate sensitivity and specificity for multiple infections and pulmonary infections. CONCLUSION This umbrella analysis indicates that NGS is a promising technique for diagnosing pneumocystis pneumonia and periprosthetic/prosthetic joint infection with excellent sensitivity and specificity. More high-quality original research and SRs are needed to verify the current findings.
Collapse
Affiliation(s)
- Hong Cao
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Yan Chen
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Long Ge
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Joey Sum-Wing Kwong
- Global Health Nursing, Graduate School of Nursing Science, St. Luke's International University, 10-1 Akashi-Cho, Chuo-Ku, Tokyo, 104-0044, Japan
| | - Honghao Lai
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Fangfang Hu
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, 550002, Guizhou Province, China
| | - Rui Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Huaye Zhao
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Linfang Hu
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Rui He
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Wenyi Zheng
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Jiaxing Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China.
| |
Collapse
|
3
|
Xie Y, Guo LY, Liu B, Hu HL, Hu B, Chen TM, Qian SY, Hei MY, Liu G. Pyogenic liver abscess in pediatric populations in beijing (2008-2023). BMC Infect Dis 2024; 24:745. [PMID: 39075343 PMCID: PMC11285452 DOI: 10.1186/s12879-024-09634-0] [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: 03/02/2024] [Accepted: 07/19/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Data on pyogenic liver abscess (PLA) of children in China have been limited. We aimed to summarize the clinical feather, microbiological characteristics, management, and outcome of PLA in children. METHOD We retrospectively reviewed PLA cases from January 2008 to June 2023 at Beijing Children's Hospital. Clinical characteristics, pathogens and management were analyzed. RESULTS We diagnosed 57 PLA patients in our center. The median onset age was 4.5 years and the male-to-female ratio was 1.6:1. The median diagnostic time was nine days and the median length of stay was 22 days. Twenty-eight patients (49.1%) had predisposing factors, around 71.4% of the patients had malignant hematology and primary immunodeficiency disease. Patients with underlying factors were more likely to have extrahepatic organ involvement (p = 0.024), anemia (p < 0.001), single abscess (p = 0.042), unilateral involvement (p = 0.039), and small size of the abscess (p = 0.008). Twenty-four patients (42.1%) had extrahepatic organ involvement. Pathogens were identified in 17 patients (29.8%), the most common pathogens were Klebsiella pneumoniae and Staphylococcus aureus. The positive rate of metagenomic next-generation sequencing (mNGS) was 87.5% (7/8). On multivariable analysis, the extrahepatic organ involved (p = 0.029) and hepatomegaly (p = 0.025) were two independent factors associated with poor outcomes. CONCLUSIONS PLA is usually seen in children with predisposing factors. Malignant hematology and primary immunodeficiency disease were the most common underlying diseases. Extrahepatic organ involvement and hepatomegaly are associated with poor prognosis. Increased use of mNGS could be beneficial for identifying pathogens.
Collapse
Affiliation(s)
- Yue Xie
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Ling-Yun Guo
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Bing Liu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Hui-Li Hu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Bing Hu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Tian-Ming Chen
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Su-Yun Qian
- Pediatric Intensive Care Unit, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Ming-Yan Hei
- Neonatal Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Gang Liu
- Key Laboratory of Major Diseases in Children, Ministry of Education, Department of Infectious Diseases, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China.
| |
Collapse
|
4
|
Chen J, Liu Y, Huang S, Pang Z, Wei Q, Liu Y, Qin H, Chen Y. Spinal Infections? mNGS Combined with Microculture and Pathology for Answers. Infect Drug Resist 2024; 17:3025-3034. [PMID: 39050835 PMCID: PMC11268561 DOI: 10.2147/idr.s466738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction This study evaluates the efficacy of metagenomic next-generation sequencing (mNGS) in diagnosing spinal infections and developing therapeutic regimens that combine mNGS, microbiological cultures, and pathological investigations. Methods Data were collected from 108 patients with suspected spinal infections between January 2022 and December 2023. Lesion tissues were obtained via C-arm assisted puncture or open surgery for mNGS, conventional microbiological culture, and pathological analysis. Personalized antimicrobial therapies were tailored based on these findings, with follow-up evaluations 7 days postoperatively. The sensitivity and specificity of mNGS were assessed, along with its impact on treatment and prognosis. Results mNGS showed a significantly higher positive detection rate (61.20%) compared to conventional microbiological culture (30.80%) and PCT (28%). mNGS demonstrated greater sensitivity (79.41%) and negative predictive value (63.16%) than cultures (25% and 22.58%, respectively), with no significant difference in specificity and positive predictive value. Seven days post-surgery, a significant reduction in neutrophil percentage (NEUT%) was observed, though decreases in white blood cell count (WBC), erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) were not statistically significant. At the last follow-up, significant improved in Visual Analogue Scale (VAS) scores, Oswestry Disability Index (ODI), and Japanese Orthopaedic Association (JOA) scores were noted. Conclusion mNGS outperforms traditional microbiological culture in pathogen detection, especially for rare and critical pathogens. Treatment protocols combining mNGS, microbiological cultures, and pathological examinations are effective and provide valuable clinical insights for treating spinal infections.
Collapse
Affiliation(s)
- Jiayi Chen
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Yonghong Liu
- Department of Preventive Health Care, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Shengsheng Huang
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Zixiang Pang
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Qian Wei
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Yuzhen Liu
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Hongyuan Qin
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Yuanming Chen
- Department of Spinal Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| |
Collapse
|
5
|
Hong D, Wang P, Xu Y, Xu S, Yu L, Tong Z, Li W, Qin K, Ke L. Metagenomic Next-Generation Sequencing-Based Fine-Needle Aspiration in Patients With Suspected Infected Pancreatic Necrosis. Clin Transl Gastroenterol 2024; 15:e00726. [PMID: 38870091 PMCID: PMC11272294 DOI: 10.14309/ctg.0000000000000726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
INTRODUCTION Fine-needle aspiration (FNA) is no longer recommended for diagnosing infected pancreatic necrosis (IPN) due to a high false-negative rate. Metagenomic next-generation sequencing (mNGS) is a valuable tool for identifying potential pathogens. We hypothesized that adding mNGS to the standard FNA procedure may increase diagnostic accuracy. METHODS This is a prospective, single-arm feasibility study enrolling patients with acute necrotizing pancreatitis complicated by suspected IPN. Computed tomography-guided FNA was performed immediately after enrollment, and the drainage samples were subjected to culture and mNGS assays simultaneously. Confirmatory IPN within the following week of the index FNA procedure was the reference standard. The diagnostic performance of FNA-mNGS and the impact of mNGS results on treatment were evaluated. Historical controls were used for comparison of clinical outcomes. RESULTS There was no significant difference between mNGS and culture in the positive rate (75% vs 70%, P = 0.723). The accuracy of FNA-mNGS was 80.0%, with a sensitivity of 82.35%, specificity of 66.67%, positive predictive value of 93.3%, and negative predictive value of 40.0%. The results of the mNGS led to treatment change in 16 of 20 patients (80%), including implementing percutaneous catheter drainage (n = 7), expanding antibiotic coverage (n = 2), percutaneous catheter drainage and expanding coverage (n = 4), narrowing antibiotic coverage (n = 1), and discontinuation of antibiotics (n = 2). The FNA-mNGS approach was not associated with improved clinical outcomes compared with the historical control group. DISCUSSION The addition of mNGS to standard FNA has comparable diagnostic accuracy with culture-based FNA and may not be associated with improved clinical outcomes.
Collapse
Affiliation(s)
- Donghuang Hong
- Department of Critical Care Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Peng Wang
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yao Xu
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Shan Xu
- Department of Emergency Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lei Yu
- Department of Emergency Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhihui Tong
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Weiqin Li
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
- National Institute of Healthcare Data Science, Nanjing University, Nanjing, China
| | - Kaixiu Qin
- Department of Emergency Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lu Ke
- Center of Severe Acute Pancreatitis (CSAP), Department of Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
- National Institute of Healthcare Data Science, Nanjing University, Nanjing, China
| |
Collapse
|
6
|
Shi P, Liu J, Liang A, Zhu W, Fu J, Wu X, Peng Y, Yuan S, Wu X. Application of metagenomic next-generation sequencing in optimizing the diagnosis of ascitic infection in patients with liver cirrhosis. BMC Infect Dis 2024; 24:503. [PMID: 38769522 PMCID: PMC11107059 DOI: 10.1186/s12879-024-09396-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/09/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is an emerging technique for the clinical diagnosis of infectious disease that has rarely been used for the diagnosis of ascites infection in patients with cirrhosis. This study compared mNGS detection with conventional culture methods for the on etiological diagnosis of cirrhotic ascites and evaluated the clinical effect of mNGS. METHODS A total of 109 patients with ascites due to cirrhosis were included in the study. We compared mNGS with conventional culture detection by analyzing the diagnostic results, pathogen species and clinical effects. The influence of mNGS on the diagnosis and management of ascites infection in patients with cirrhosis was also evaluated. RESULTS Ascites cases were classified into three types: spontaneous bacterial peritonitis (SBP) (16/109, 14.7%), bacterascites (21/109, 19.3%) and sterile ascites (72/109, 66.1%). In addition, 109 patients were assigned to the ascites mNGS-positive group (80/109, 73.4%) or ascites mNGS-negative group (29/109, 26.6%). The percentage of positive mNGS results was significantly greater than that of traditional methods (73.4% vs. 28.4%, P < 0.001). mNGS detected 43 strains of bacteria, 9 strains of fungi and 8 strains of viruses. Fourteen bacterial strains and 3 fungal strains were detected via culture methods. Mycobacteria, viruses, and pneumocystis were detected only by the mNGS method. The mNGS assay produced a greater polymicrobial infection rate than the culture method (55% vs. 16%). Considering the polymorphonuclear neutrophil (PMN) counts, the overall percentage of pathogens detected by the two methods was comparable, with 87.5% (14/16) in the PMN ≥ 250/mm3 group and 72.0% (67/93) in the PMN < 250/mm3 group (P > 0.05). Based on the ascites PMN counts combined with the mNGS assay, 72 patients (66.1%) were diagnosed with ascitic fluid infection (AFI) (including SBP and bacterascites), whereas based on the ascites PMN counts combined with the culture assay, 37 patients (33.9%) were diagnosed with AFI (P < 0.05). In 60 (55.0%) patients, the mNGS assay produced positive clinical effects; 40 (85.7%) patients had their treatment regimen adjusted, and 48 patients were improved. The coincidence rate of the mNGS results and clinical findings was 75.0% (60/80). CONCLUSIONS Compared with conventional culture methods, mNGS can improve the detection rate of ascites pathogens, including bacteria, viruses, and fungi, and has significant advantages in the diagnosis of rare pathogens and pathogens that are difficult to culture; moreover, mNGS may be an effective method for improving the diagnosis of ascites infection in patients with cirrhosis, guiding early antibiotic therapy, and for reducing complications related to abdominal infection. In addition, explaining mNGS results will be challenging, especially for guiding the treatment of infectious diseases.
Collapse
Affiliation(s)
- Pei Shi
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Juan Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - An Liang
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Wentao Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Jiwei Fu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Xincheng Wu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Yuchen Peng
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China
| | - Songsong Yuan
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China.
| | - Xiaoping Wu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanchang University, No.17 Yongwaizheng Street, Donghu District, Nanchang, Jiangxi Province, China.
| |
Collapse
|
7
|
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
|
8
|
Yang T, Fu Y. Trichosporon asahii co-infection with Pneumocystis jiroveci in a renal transplant patient. IDCases 2024; 36:e01951. [PMID: 38707649 PMCID: PMC11066508 DOI: 10.1016/j.idcr.2024.e01951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/06/2024] [Accepted: 04/14/2024] [Indexed: 05/07/2024] Open
Abstract
Trichosporon asahii is considered an opportunistic pathogen, capable of causing superficial infections in humans and invasive deep-seated infections in immunocompromised hosts. Pneumocystis jirovecii can cause life-threatening pneumonia in immunosuppressed patients. Both Trichosporon and Pneumocystis jirovecii are highly lethal in immunocompromised individuals. Here we present a case of invasive Trichosporon asahii co-infection with Pneumocystis jiroveci in a renal transplant patient.
Collapse
Affiliation(s)
- Tingting Yang
- Department of Laboratory Medicine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Yajie Fu
- Department of Laboratory Medicine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310006, China
| |
Collapse
|
9
|
Zhang D, Cheng Y, Ji Y, Miao Q, Chen B, Wang J, Wu G, Yuan C, Zheng G, Liu H, Qiu X, Gong J, Ba H, Pan L, Ma X, Qi Y, Shi Y, Zhang Q, Li D, Xu Y. A training program for improving the capacity of infection high-throughput sequencing and diagnosis in China. BMC MEDICAL EDUCATION 2024; 24:142. [PMID: 38355463 PMCID: PMC10865699 DOI: 10.1186/s12909-024-05100-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Infectious diseases are a serious threat to human especially since the COVID-19 outbreak has proved the importance and urgency of their diagnosis and treatment again. Metagenomic next-generation sequencing (mNGS) has been widely used and recognized in clinical and carried out localized testing in hospitals. Increasing the training of mNGS detection technicians can enhance their professional quality and more effectively realize the application value of the hospital platform. METHODS Based on the initial theoretical understanding and practice of the mNGS platform for localization construction, we have designed a training program to enhance the ability of technicians to detect pathogens by utilizing mNGS, and hence to conduct training practices nationwide. RESULTS Until August 30, 2022, the page views of online classes have reached 51,500 times and 6 of offline small-scale training courses have been conducted. A total of 67 trainees from 67 hospitals have participated in the training with a qualified rate of 100%. After the training course, the localization platform of 1 participating hospital has been put into use, 2 have added the mNGS localization platform for admission, among which 3 have expressed strong intention of localization. CONCLUSIONS This study focuses on the training procedures and practical experience of the project which is the first systematic standardized program of mNGS in the world. It solves the training difficulties in the current industry, and effectively promotes the localization construction and application of mNGS in hospitals. It has great development potential in the future and is worth further promotion.
Collapse
Affiliation(s)
- Dong Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
| | - Yunfeng Cheng
- Zhongshan Hospital, Fudan University, 180 Fenglin Rd, 200032, Shanghai, China
| | - Yuan Ji
- Zhongshan Hospital, Fudan University, 180 Fenglin Rd, 200032, Shanghai, China
| | - Qing Miao
- Zhongshan Hospital, Fudan University, 180 Fenglin Rd, 200032, Shanghai, China
| | - Bojiang Chen
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Jing Wang
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, 210009, Nanjing, Jiangsu, China
| | - Chenyan Yuan
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, 210009, Nanjing, Jiangsu, China
| | - Guangjuan Zheng
- Genetic Testing Lab, The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Han Liu
- Genetic Testing Lab, The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinmin Qiu
- Genetic Testing Lab, The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jie Gong
- Department of Clinical Laboratory, Wuhan Center for Clinical Laboratory, Wuhan, Hubei, China
| | - Hongping Ba
- Department of Clinical Laboratory, Wuhan Center for Clinical Laboratory, Wuhan, Hubei, China
| | - Liping Pan
- Department of Clinical Laboratory, Wuhan Center for Clinical Laboratory, Wuhan, Hubei, China
| | - Xiaoling Ma
- Department of Laboratory Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230000, Hefei, Anhui, China
| | - Yingjie Qi
- Department of Laboratory Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230000, Hefei, Anhui, China
| | - Yuru Shi
- Department of Laboratory Medicine, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, 230000, Hefei, Anhui, China
| | - Qi Zhang
- Beijing life oasis public service center, Beijing, China
| | - Dan Li
- BGI Genomics, 518083, Shenzhen, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
| |
Collapse
|
10
|
Chen S, Wang C, Zou Y, Zong Z, Xue Y, Jia J, Dong L, Zhao L, Chen L, Liu L, Chen W, Huang H. Tuberculosis-targeted next-generation sequencing and machine learning: An ultrasensitive diagnostic strategy for paucibacillary pulmonary tuberculosis and tuberculous meningitis. Clin Chim Acta 2024; 553:117697. [PMID: 38145644 DOI: 10.1016/j.cca.2023.117697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Existing diagnostic approaches for paucibacillary tuberculosis (TB) are limited by the low sensitivity of testing methods and difficulty in obtaining suitable samples. METHODS An ultrasensitive TB diagnostic strategy was established, integrating efficient and specific TB targeted next-generation sequencing and machine learning models, and validated in clinical cohorts to test plasma cfDNA, cerebrospinal fluid (CSF) DNA collected from tuberculous meningitis (TBM) and pediatric pulmonary TB (PPTB) patients. RESULTS In the detection of 227 samples, application of the specific thresholds of CSF DNA (AUC = 0.974) and plasma cfDNA (AUC = 0.908) yielded sensitivity of 97.01 % and the specificity of 95.65 % in CSF samples and sensitivity of 82.61 % and specificity of 86.36 % in plasma samples, respectively. In the analysis of 44 paired samples from TBM patients, our strategy had a high concordance of 90.91 % (40/44) in plasma cfDNA and CSF DNA with both sensitivity of 95.45 % (42/44). In the PPTB patient, the sensitivity of the TB diagnostic strategy yielded higher sensitivity on plasma specimen than Xpert assay on gastric lavage (28.57 % VS. 15.38 %). CONCLUSIONS Our TB diagnostic strategy provides greater detection sensitivity for paucibacillary TB, while plasma cfDNA as an easily collected specimen, could be an appropriate sample type for PTB and TBM diagnosis.
Collapse
Affiliation(s)
- Suting Chen
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Congli Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yijun Zou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaojing Zong
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China; Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi 563001, China
| | - Yi Xue
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Junnan Jia
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Lingling Dong
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Liping Zhao
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Lu Chen
- Beijing Macroµ-test Bio-Tech Co., Ltd., Beijing 101300, China
| | - Licheng Liu
- Beijing Macroµ-test Bio-Tech Co., Ltd., Beijing 101300, China
| | - Weijun Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China.
| |
Collapse
|
11
|
Fu Z, Ai J, Zhang H, Cui P, Xu T, Zhang Y, Zhang Y, Wu H, Shen A, Lin K, Zhang M, Qiu C, Jiang N, Zhou Y, Zhang W. Pathogen quantitative efficacy of different spike-in internal controls and clinical application in central nervous system infection with metagenomic sequencing. Microbiol Spectr 2023; 11:e0113923. [PMID: 37982612 PMCID: PMC10714923 DOI: 10.1128/spectrum.01139-23] [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: 03/27/2023] [Accepted: 10/01/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Metagenomic next-generation sequencing (mNGS) has been used broadly for pathogens detection of infectious diseases. However, there is a lack of method for the absolute quantitation of pathogens by mNGS. We compared the quantitative efficiency of three mNGS internal controls (ICs) Thermus thermophilus, T1 phages, and artificial DNA sequence and developed the most applicable strategies for pathogen quantitation via mNGS in central nervous system infection. The IC application strategy we developed will enable mNGS analysis to assess the pathogen load simultaneously with the detection of pathogens, which should provide critical information for quick decision-making of treatment as well as clinical prognosis.
Collapse
Affiliation(s)
- Zhangfan Fu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingwen Ai
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peng Cui
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tao Xu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yumeng Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Honglong Wu
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Ao Shen
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
| | - Ke Lin
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Miaoqu Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chao Qiu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ning Jiang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Zhou
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, China
| |
Collapse
|
12
|
Huang W, Wang F, Cai Q, Xu H, Hong D, Wu H, Zhou L, Hu L, Lu Y. Epidemiological and clinical characteristics of psittacosis among cases with complicated or atypical pulmonary infection using metagenomic next-generation sequencing: a multi-center observational study in China. Ann Clin Microbiol Antimicrob 2023; 22:80. [PMID: 37679777 PMCID: PMC10486088 DOI: 10.1186/s12941-023-00631-w] [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: 04/26/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Chlamydia psittaci (C. psittaci) causes parrot fever in humans. Development of metagenomic next-generation sequencing (mNGS) enables the identification of C. psittaci. METHODS This study aimed to determine the epidemiological and clinical characteristics of parrot fever cases in China. A multi-center observational study was conducted in 44 tertiary and secondary hospitals across 14 provinces and municipalities between April 2019 and October 2021. RESULTS A total of 4545 patients with complicated or atypical pulmonary infection were included in the study, among which the prevalence of C. psittaci was determined to be 2.1% using mNGS. The prevalence of C. psittaci was further determined across demographic groups and types of specimens. It was significantly higher in patients with senior age (2.6% in those > 50 years), winter-spring (3.6%; particularly in December, January, and February), and southwestern (3.4%) and central and southern China (2.7%) (each P < 0.001). Moreover, the prevalence was the highest in bronchoalveolar lavage fluid (BALF) (2.9%), compared with sputum (1.1%) and peripheral blood specimens (0.9%). Additionally, co-infection of principal microorganisms was compared. Certain microorganisms were more likely to co-infect in parrot fever cases, such as Candida albicans in BALF (26.7%) and peripheral blood (6.3%), compared with non-parrot fever cases (19.7% and 1.3%); however, they did not significantly differ (each P > 0.05). CONCLUSION Parrot fever remains low in patients with complicated or atypical pulmonary infection. It is likely to occur in winter-spring and southwestern region in China. BALF may be the optimal specimen in the application of mNGS. Co-infection of multiple microorganisms should be further considered.
Collapse
Affiliation(s)
- Weifeng Huang
- Department of Intensive Care Medicine, The Sixth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fengge Wang
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc, Shanghai, China
| | - Huiliang Xu
- Department of Respiratory, Nanxiang Hospital of Jiading district, Shanghai, China
| | - Dengwei Hong
- Genoxor Medical Science and Technology Inc, Shanghai, China
| | - Han Wu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, Fudan University School of Public Health, Shanghai, China
| | - Lu Zhou
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, Fudan University School of Public Health, Shanghai, China
| | - Linjie Hu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, Fudan University School of Public Health, Shanghai, China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, Fudan University School of Public Health, Shanghai, China
| |
Collapse
|
13
|
Su ZQ, Rao WY, Pan XY, Tang JX, Fan MY, Chen XB, Li SY. Multiple Lung Cavity Lesions, Thoracic Wall Abscess and Vertebral Destruction Caused by Streptococcus constellatus Infection: A Case Report. Infect Drug Resist 2023; 16:5329-5333. [PMID: 37601557 PMCID: PMC10439794 DOI: 10.2147/idr.s416483] [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: 05/01/2023] [Accepted: 07/26/2023] [Indexed: 08/22/2023] Open
Abstract
Disseminated infection caused by Streptococcus constellatus was seldom occurred. We reported a case of Streptococcus constellatus infection, presenting as multiple pulmonary cavities, thoracic wall abscess and vertebral destruction. The 37-year-old male had recurrent fever, chest wall swelling and pain, and lower limb numbness, he had weak physical condition and previously suffered from poorly controlled diabetes and severe periodontal disease for 3 years. Definite diagnosis of Streptococcus constellatus infection was made by metagenomic next‑generation sequencing (mNGS) in abscess drainage fluid. Systemic antibiotics and thoracic wall drainage were given, and the pulmonary cavity and the thoracic intermuscular abscess were significantly decreased. Few to no study reported the disseminated infection (pulmonary cavities, thoracic wall abscess and vertebral destruction) caused by Streptococcus constellatus. This case report highlighted the importance of mNGS for accurate diagnosis, as well as the timely drainage and antibiotics for effective treatment of Streptococcus constellatus infection.
Collapse
Affiliation(s)
- Zhu-Quan Su
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wan-Yuan Rao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xiao-Yi Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jia-Xin Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ming-Yue Fan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xiao-Bo Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Shi-Yue Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| |
Collapse
|
14
|
Xu J, Zhou P, Liu J, Zhao L, Fu H, Han Q, Wang L, Wu W, Ou Q, Ma Y, He J. Utilizing Metagenomic Next-Generation Sequencing (mNGS) for Rapid Pathogen Identification and to Inform Clinical Decision-Making: Results from a Large Real-World Cohort. Infect Dis Ther 2023; 12:1175-1187. [PMID: 36988865 PMCID: PMC10147866 DOI: 10.1007/s40121-023-00790-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
INTRODUCTION Clinical metagenomic next-generation sequencing (mNGS) has proven to be a powerful diagnostic tool in pathogen detection. However, its clinical utility has not been thoroughly evaluated. METHODS In this single-center prospective study at the First Affiliated Hospital of Soochow University, a total of 228 samples from 215 patients suspected of having acute or chronic infections between June 2018 and December 2018 were studied. Samples that met the mNGS quality control (QC) criteria (N = 201) were simultaneously analyzed using conventional tests (CTs), including multiple clinical microbiological tests and real-time PCR (if applicable). RESULTS Pathogen detection results of mNGS in the 201 QC-passed samples were compared to CTs and exhibited a sensitivity of 98.8%, specificity of 38.5%, and accuracy of 87.1%. Specifically, 109 out of 160 (68.1%) CT+/mNGS+ samples exhibited concordant results at the species/genus level, 25 samples (15.6%) showed overlapping results, while the remaining 26 samples (16.3%) had discordant results between the CT and mNGS assays. In addition, mNGS could identify pathogens at the species level, whereas only the genera of some pathogens could be identified by CT. In this cohort, mNGS results were used to guide treatment plans in 24 out of 41 cases that had available follow-up information, and the symptoms were improved in over 70% (17/24) of them. CONCLUSION Our data demonstrated the analytic performance of our mNGS pipeline for pathogen detection using a large clinical cohort and strongly supports the notion that in clinical practice, mNGS represents a valuable supplementary tool to CTs to rapidly determine etiological factors of various types of infection and to guide treatment decision-making.
Collapse
Affiliation(s)
- Jie Xu
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China
| | - Peng Zhou
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Jia Liu
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Lina Zhao
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Hailong Fu
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China
| | - Qingzhen Han
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Lin Wang
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Weiwei Wu
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Qiuxiang Ou
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Yutong Ma
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Jun He
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China.
- HLA Laboratory of Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, The First Affiliated Hospital of Soochow University, 13/F (West), Hospital Comprehensive Building, No.899 Ping Hai Road, Suzhou, 215031, Jiangsu, China.
| |
Collapse
|
15
|
Zhang G, Zhang H, Hu X, Xu D, Tang B, Tang M, Liu S, Li Y, Xu W, Guo C, Gao Q. Clinical application value of metagenomic next-generation sequencing in the diagnosis of spinal infections and its impact on clinical outcomes. Front Cell Infect Microbiol 2023; 13:1076525. [PMID: 36844401 PMCID: PMC9945583 DOI: 10.3389/fcimb.2023.1076525] [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: 10/21/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
This study aimed to evaluate the impact of precise treatment administered according to the results of metagenomic next-generation sequencing (mNGS) on the clinical outcomes of patients with spinal infections. In this multicenter retrospective study, the clinical data of 158 patients with spinal infections who were admitted to Xiangya Hospital Central South University, Xiangya Boai Rehabilitation Hospital, The First Hospital of Changsha, and Hunan Chest Hospital from 2017 to 2022 were reviewed. Among these 158 patients, 80 patients were treated with targeted antibiotics according to the mNGS results and were assigned to the targeted medicine (TM) group. The remaining 78 patients with negative mNGS results and those without mNGS and negative microbial culture results were treated with empirical antibiotics and assigned to the empirical drug (EM) group. The impact of targeted antibiotics based on the mNGS results on the clinical outcomes of patients with spinal infections in the two groups was analyzed. The positive rate of mNGS for diagnosing spinal infections was significantly higher than that of microbiological culture (X 2=83.92, P<0.001), procalcitonin (X 2=44.34, P<0.001), white blood cells (X 2=89.21, P < 0.001), and IGRAs (Interferon-gamma Release Tests) (X 2 = 41.50, P < 0.001). After surgery, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) showed a decreasing trend in the patients with spinal infections in both the TM and EM groups. The decrease in CRP was more obvious in the TM group than in the EM group at 7, 14 days, 3, and 6 months after surgery (P<0.05). The decrease in ESR was also significantly obvious in the TM group compared with the EM group at 1 and 6 months after surgery (P<0.05). The time taken for CRP and ESR to return to normal in the TM group was significantly shorter than that in the EM group (P<0.05). There was no significant difference in the incidence of poor postoperative outcomes between the two groups. The positive rate of mNGS for the diagnosis of spinal infection is significantly higher than that of traditional detection methods. The use of targeted antibiotics based on mNGS results could enable patients with spinal infections to achieve a faster clinical cure.
Collapse
Affiliation(s)
- Guang Zhang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hongqi Zhang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - XiaoJiang Hu
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Dongcheng Xu
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Bo Tang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Mingxing Tang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Shaohua Liu
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yanbing Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wen Xu
- Department of Scientific Affaires,Guangzhou Sagene Biotechnology Company, Limited, Guangzhou, China
| | - Chaofeng Guo
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qile Gao
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Qile Gao,
| |
Collapse
|
16
|
Shi Y, Wu J, Liu T, Li Y, Liu Y, Gu Y, Qi Y. Analysis of Metagenomic Next-Generation Sequencing Results of 25 Pus Samples. Infect Drug Resist 2022; 15:6515-6524. [DOI: 10.2147/idr.s385925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
|
17
|
Zhang J, Gao L, Zhu C, Jin J, Song C, Dong H, Li Z, Wang Z, Chen Y, Yang Z, Tan Y, Wang L. Clinical value of metagenomic next-generation sequencing by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid in suspected community-acquired pneumonia patients. Front Cell Infect Microbiol 2022; 12:1021320. [PMID: 36237436 PMCID: PMC9551279 DOI: 10.3389/fcimb.2022.1021320] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
At present, metagenomic next-generation sequencing (mNGS) based on Illumina platform has been widely reported for pathogen detection. There are few studies on the diagnosis of major pathogens and treatment regulation using mNGS based on Illumina versus Nanopore. We aim to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid (BALF) in suspected community-acquired pneumonia (CAP) patients. BALF samples collected from 66 suspected CAP patients within 48 hours of hospitalization were divided into two parts, one for conventional culture and the other for mNGS by two platforms (Illumina and Nanopore). The clinical value based on infection diagnosis, diagnostic performance for main pathogens and treatment guidance were assessed. More types of species were detected by Nanopore than Illumina, especially in viruses, fungus and mycobacterium. Illumina and Nanopore showed similar detectability in bacterium except for mycobacterium tuberculosis complex/nontuberculosis mycobacteria. Pathogenic infection was established or excluded in 53 of 66 patients. There was little difference in the coincidence rate between Illumina and Nanopore with the clinical diagnosis, but both were superior to the culture (57.81%, 59.38%, 25%, respectively). Compared with Illumina, the diagnostic area under the curve of Nanopore was higher in fungi, but lower in bacteria and Chlamydia psittaci. There was no statistically significant difference between Illumina and Nanopore in guiding drug treatment (56.1% vs. 50%, p=0.43), but both were superior to the culture (56.1% vs. 28.8%, p=0.01; 50% vs. 28.8%, p=0.01). Single inflammatory indicators could not be used to determine whether the patients with culture-negative BALF were established or excluded from infection. The species detected at 1 h and 4 h by Nanopore were consistent to some extent, and its turn-around time (TAT) was significantly shorter than Illumina (p<0.01). Illumina and Nanopore both have its own advantages in pathogenic diagnosis and play similar roles in infection diagnosis and guiding clinical treatment. Nanopore has a relatively short TAT, which may be promising in rapid etiological diagnosis of acute and critically ill patients.
Collapse
Affiliation(s)
- Jing Zhang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Lin Gao
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Chi Zhu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Jiajia Jin
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Hang Dong
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Zhenzhong Li
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Zheng Wang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yubao Chen
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zhenhua Yang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yan Tan
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Li Wang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| |
Collapse
|
18
|
Wang Y, Hu X, Yang L, Chen C, Cheng H, Hu H, Liang W, Tong Y, Wang M, Wang H. Application of High-Throughput Sequencing Technology in the Pathogen Identification of Diverse Infectious Diseases in Nephrology Departments. Diagnostics (Basel) 2022; 12:diagnostics12092128. [PMID: 36140529 PMCID: PMC9497786 DOI: 10.3390/diagnostics12092128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Objective: The purpose of this study was to explore the clinical applications of high-throughput sequencing (HTS) in the identification of pathogens in patients with urinary tract infection (UTI), peritoneal dialysis-associated peritonitis (PDAP), central venous catheter related blood infections (CRBIs), and lung infections in the nephrology department. Methods: Midstream urine samples from 112 patients with UTI, peritoneal fluid samples from 67 patients with PDAP, blood samples from 15 patients with CRBI, and sputum specimens from 53 patients with lung infection were collected. The HTS and ordinary culture methods were carried out in parallel to identify the pathogens in each sample. Pathogen detection positive rate and efficacy were compared between the two methods. Results: The pathogen positive detection rates of HTS in UTI, PDAP, CRBI, and lung infection were strikingly higher than those of the culture method (84.8% vs. 35.7, 71.6% vs. 23.9%, 75% vs. 46.7%, 84.9% vs. 5.7%, p < 0.05, respectively). HTS was superior to the culture method in the sensitivity of detecting bacteria, fungi, atypical pathogens, and mixed microorganisms in those infections. In patients who had empirically used antibiotics before the test being conducted, HTS still exhibited a considerably higher positive rate than the culture method (81.6% vs. 39.0%, 68.1% vs. 14.9%, 72.7% vs. 36.4%, 83.3% vs. 4.2%, p < 0.05, respectively). Conclusions: HTS is remarkably more efficient than the culture method in detecting pathogens in diverse infectious diseases in nephrology, and is particularly potential in identifying the pathogens that are unable to be identified by the common culture method, such as in cases of complex infection with specific pathogens or subclinical infection due to preemptive use of antibiotics.
Collapse
Affiliation(s)
- Yujuan Wang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Xiaoyi Hu
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Lianhua Yang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Cheng Chen
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Hui Cheng
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Haiyun Hu
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Wei Liang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Yongqing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
| | - Ming Wang
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
- Correspondence: (M.W.); (H.W.)
| | - Huiming Wang
- Department of Nephrology, Renmin Hospital of Wuhan University, Jiefang Road 238, Wuchang District, Wuhan 430060, China
- Correspondence: (M.W.); (H.W.)
| |
Collapse
|
19
|
Tang J, Tan W, Luo L, Xu H, Li N. Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pneumonia Caused by Chlamydia psittaci. Microbiol Spectr 2022; 10:e0238421. [PMID: 35938720 PMCID: PMC9431268 DOI: 10.1128/spectrum.02384-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/06/2022] [Indexed: 11/20/2022] Open
Abstract
Psittacosis is an uncommon disease which mainly presents as community-acquired pneumonia (CAP). We aim to apply metagenomic next-generation sequencing (mNGS) as a promising tool in the diagnosis of psittacosis pneumonia and to describe its clinical spectrum to provide physicians with a better understanding and recognition of this disease. Thirteen cases of psittacosis pneumonia were diagnosed by using mNGS. A retrospective analysis of the data on clinical manifestations, laboratory data, computed tomography (CT) images, new diagnosis tools, treatments, and outcomes was summarized. These patients had common symptoms of fever and weakness; some had poor appetite, cough, myalgia, and headache. Ten patients developed acute respiratory distress syndrome (ARDS), among which six patients were severe pneumonia cases and needed ventilator therapy. Most patients got psittacosis pneumonia during the cold season. Ten cases were sporadic, but three were family clustering. All of the 13 patients were traced to an exposure history to birds, cat, or poultry, among which 2 only touched the innards of killed poultry before cooking, which may be an atypical exposure history not been reported before, to our knowledge. Most patients had various degrees of liver dysfunction. Air-space consolidations, along with ground-glass opacities and reticular shadows, were detected on chest CT scan. mNGS takes 48 to 72 h to provide results and helps to diagnose psittacosis. After being diagnosed by mNGS, with effective medicines, all patients finally had complete recoveries. The use of mNGS can improve the diagnostic rate of psittacosis pneumonia and shorten the course of disease control. IMPORTANCE Psittacosis pneumonia is easily underdiagnosed and misdiagnosed. In this study, we use mNGS in the diagnosis of psittacosis pneumonia. We found this disease is prone in the cold season, and touching the innards of killed poultry during cooking may be an atypical exposure history which has not been reported before to our knowledge. There are sporadic cases and family outbreak cases as well. Except for typical symptoms of fever and weakness, headache may be the main and only symptom in some patients. The rate of severe pneumonia is high among inpatients with psittacosis pneumonia, and the incidence of hepatic involvements is also high. Psittacosis pneumonia can be cured if the diagnosis is accurate and in time, even if it is severe pneumonia on admission. Some problems worthy of our attention about psittacosis pneumonia were put forward, such as its sick season, special exposure history, the rate of severe disease, and the high cure rate. mNGS can quickly and objectively detect more rare pathogenic microorganisms in clinical specimens without the need for specific amplification and has an advantage in the diagnosis of rare pathogenic bacteria in difficult cases such as psittacosis pneumonia. The use of mNGS can improve the accuracy and reduce the delay in the diagnosis of psittacosis, which shortens the course of disease control.
Collapse
Affiliation(s)
- Junli Tang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Wanmei Tan
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Lingxin Luo
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Huan Xu
- Vision Medicals Center for Infection Disease, Guangzhou, People’s Republic of China
| | - Na Li
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| |
Collapse
|
20
|
Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: a Multicenter Retrospective Study. Microbiol Spectr 2022; 10:e0247321. [PMID: 35943274 PMCID: PMC9431624 DOI: 10.1128/spectrum.02473-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has been gradually applied to clinical practice due to its unbiased characteristics of pathogen detection. However, its diagnostic performance and clinical value in suspected pulmonary infection need to be evaluated. We systematically reviewed the clinical data of 246 patients with suspected pulmonary infection from 4 medical institutions between January 2019 and September 2021. The diagnostic performances of mNGS and conventional testing (CT) were systematically analyzed based on bronchoalveolar lavage fluid (BALF). The impacts of mNGS and CT on diagnosis modification and treatment adjustment were also assessed. The positive rates of mNGS and CT were 47.97% and 23.17%, respectively. The sensitivity of mNGS was significantly higher than that of CT (53.49% versus 23.26%, P < 0.01), especially for infections of Mycobacterium tuberculosis (67.86% versus 17.86%, P < 0.01), atypical pathogens (100.00% versus 7.14%, P < 0.01), viruses (92.31% versus 7.69%, P < 0.01), and fungi (78.57% versus 39.29%, P < 0.01). The specificity of mNGS was superior to that of CT, with no statistical difference (90.32% versus 77.42%, P = 0.167). The positive predictive value (PPV) and negative predictive value (NPV) of mNGS were 97.46% and 21.88%, respectively. Diagnosis modification and treatment adjustment were conducted in 32 (32/246, 13.01%) and 23 (23/246, 9.35%) cases, respectively, according to mNGS results only. mNGS significantly improved the diagnosis of suspected pulmonary infection, especially infections of M.tuberculosis, atypical pathogens, viruses, and fungi, and it demonstrated the pathogen distribution of pulmonary infections. It is expected to be a promising microbiological detection and diagnostic method in clinical practice. IMPORTANCE Pulmonary infection is a heterogeneous and complex infectious disease with high morbidity and mortality worldwide. In clinical practice, a considerable proportion of the etiology of pulmonary infection is unclear, microbiological diagnosis being challenging. Metagenomic next-generation sequencing detects all nucleic acids in a sample in an unbiased manner, revealing the microbial community environment and organisms and improving the microbiological detection and diagnosis of infectious diseases in clinical settings. This study is the first multicenter, large-scale retrospective study based entirely on BALF for pathogen detection by mNGS, and it demonstrated the superior performance of mNGS for microbiological detection and diagnosis of suspected pulmonary infection, especially in infections of Mycobacterium tuberculosis, atypical pathogens, viruses, and fungi. It also demonstrated the pathogen distribution of pulmonary infections in the real world, guiding targeted treatment and improving clinical management and prognoses.
Collapse
|
21
|
Liang M, Fan Y, Zhang D, Yang L, Wang X, Wang S, Xu J, Zhang J. Metagenomic next-generation sequencing for accurate diagnosis and management of lower respiratory tract infections. Int J Infect Dis 2022; 122:921-929. [PMID: 35908723 DOI: 10.1016/j.ijid.2022.07.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/07/2022] [Accepted: 07/23/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in patients with suspected lower respiratory tract infections (LRTIs). METHODS This retrospective study reviewed patients with suspected LRTIs in Wuhan Union Hospital. Data including demographic, laboratory, and radiological profiles; treatment; and outcomes were recorded and analyzed. RESULTS mNGS identified pathogenic microbes in 100/140 (71.4%) patients, although 135 (96.4%) had received empiric antibiotic treatment before the mNGS tests. Single bacterial infection (35/100, 35%) was the most common type of infection in patients with positive mNGS results, followed by single fungal infection (14/100, 14%), bacterial-viral co-infection (14/100, 14%), single viral infection (12/100, 12%), bacterial-fungal co-infection (9/100, 9%), fungal-viral co-infection (9/100, 9%), and bacterial-fungal-viral co-infection (7/100, 7%). Moreover, compared with culture test, mNGS showed higher sensitivity (63/85, 74.1% vs. 22/85, 25.9% P=0.001) and lower processing time (24 h vs 48 h). Antibiotic treatment was adjusted or confirmed based on the mNGS results in 123 (87.9%) patients, including 5 (3.6%), 33 (23.6%) and 85 (60.7%) patients in whom treatment was downgraded, upgraded and unchanged, respectively, and almost all patients, regardless of escalation, de-escalation, or no change in treatment, showed significant improvement in clinical symptoms and inflammatory indicators. Additionally, 17 (12.1%) patients were referred to Wuhan Pulmonary Hospital for further treatment because of confirmed or suspected tuberculosis. CONCLUSIONS mNGS could be a promising technique for microbiological diagnosis and antibiotic management, potentially improving outcomes of patients.
Collapse
Affiliation(s)
- Mengyuan Liang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Yamin Fan
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Dongmei Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Lian Yang
- Department of Radiology, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Xiaorong Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Sufei Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Juanjuan Xu
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China.
| | - Jianchu Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China.
| |
Collapse
|
22
|
Sun L, Zhang S, Yang Z, Yang F, Wang Z, Li H, Li Y, Sun T. Clinical Application and Influencing Factor Analysis of Metagenomic Next-Generation Sequencing (mNGS) in ICU Patients With Sepsis. Front Cell Infect Microbiol 2022; 12:905132. [PMID: 35909965 PMCID: PMC9326263 DOI: 10.3389/fcimb.2022.905132] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
Objective To analyze the clinical application and related influencing factors of metagenomic next-generation sequencing (mNGS) in patients with sepsis in intensive care unit (ICU). Methods The study included 124 patients with severe sepsis admitted to the ICU in the First Affiliated Hospital of Zhengzhou University from June 2020 to September 2021. Two experienced clinicians took blood mNGS and routine blood cultures of patients meeting the sepsis diagnostic criteria within 24 hours after sepsis was considered, and collection the general clinical data. Results mNGS positive rate was higher than traditional blood culture (67.74% vs. 19.35%). APACHE II score [odds ratio (OR)=1.096], immune-related diseases (OR=6.544), and hypertension (OR=2.819) were considered as positive independent factors for mNGS or culture-positive. The sequence number of microorganisms and pathogen detection (mNGS) type had no effect on prognosis. Age (OR=1.016), female (OR=5.963), myoglobin (OR=1.005), and positive virus result (OR=8.531) were independent risk factors of sepsis mortality. Adjusting antibiotics according to mNGS results, there was no statistical difference in the prognosis of patients with sepsis. Conclusion mNGS has the advantages of rapid and high positive rate in the detection of pathogens in patients with severe sepsis. Patients with high APACHE II score, immune-related diseases, and hypertension are more likely to obtain positive mNGS results. The effect of adjusting antibiotics according to mNGS results on the prognosis of sepsis needs to be further evaluated.
Collapse
Affiliation(s)
- Limin Sun
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuguang Zhang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ziyue Yang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fei Yang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongqiang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yaoguang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tongwen Sun
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Tongwen Sun,
| |
Collapse
|
23
|
Xu P, Yang K, Yang L, Wang Z, Jin F, Wang Y, Feng J. Next-Generation Metagenome Sequencing Shows Superior Diagnostic Performance in Acid-Fast Staining Sputum Smear-Negative Pulmonary Tuberculosis and Non-tuberculous Mycobacterial Pulmonary Disease. Front Microbiol 2022; 13:898195. [PMID: 35847073 PMCID: PMC9283093 DOI: 10.3389/fmicb.2022.898195] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/07/2022] [Indexed: 11/23/2022] Open
Abstract
In this study, we explored the clinical value of next-generation metagenome sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from patients with acid-fast staining (AFS) sputum smear-negative pulmonary tuberculosis (PTB) and non-tuberculous mycobacterial pulmonary disease (NTM-PD). Data corresponding to hospitalized patients with pulmonary infection admitted to the hospital between July 2018 and July 2021, who were finally diagnosed with AFS sputum smear-negative PTB and NTM-PD, were retrospectively analyzed. Bronchoscopy data as well as mNGS, Xpert, AFS (BALF analysis), and T-SPOT (blood) data, were extracted from medical records. Thereafter, the diagnostic performances of these methods with respect to PTB and NTM-PD were compared. Seventy-one patients with PTB and 23 with NTM-PD were included in the study. The sensitivities of mNGS, Xpert, T-SPOT, and AFS for the diagnosis of PTB were 94.4% (67/71), 85.9% (61/71), 64.8% (46/71), and 28.2% (20/71), respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (97.2%, 67/71). The specificity of Xpert was 100%, while those of AFS and T-SPOT were 73.9% (17/23) and 91.3% (21/23), respectively. Further, the 23 patients with NTM-PD could be identified using mNGS, and in the population with immunosuppression, the sensitivities of mNGS, Xpert, T-SPOT, and AFS were 93.5% (29/31), 80.6% (25/31), 48.4% (15/31), and 32.3% (10/31), respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (100%, 31/31). The specificities of Xpert and T-SPOT in this regard were both 100%, while that of AFS was 40% (2/5). Furthermore, using mNGS, all the NTM samples could be identified. Thus, the analysis of BALF samples using mNGS has a high accuracy in the differential diagnosis of MTB and NTM. Further, mNGS combined with Xpert can improve the detection of MTB, especially in AFS sputum smear-negative samples from patients with compromised immune states or poor responses to empirical antibiotics.
Collapse
Affiliation(s)
- Peng Xu
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Ke Yang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Lei Yang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhongli Wang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
- Department of Respiratory and Critical Care Medicine, Shandong Second Provincial General Hospital, Jinan, China
| | - Fang Jin
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Yubao Wang
- Institute of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Jing Feng
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| |
Collapse
|
24
|
Su J, Han X, Xu X, Ding W, Li M, Wang W, Tian M, Chen X, Xu B, Chen Z, Yuan J, Qin X, Lin D, Wang R, Gong Y, Pan L, Wang J, Wang M. Simultaneous Detection of Pathogens and Tumors in Patients With Suspected Infections by Next-Generation Sequencing. Front Cell Infect Microbiol 2022; 12:892087. [PMID: 35755839 PMCID: PMC9218804 DOI: 10.3389/fcimb.2022.892087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background Differential diagnosis of patients with suspected infections is particularly difficult, but necessary for prompt diagnosis and rational use of antibiotics. A substantial proportion of these patients have non-infectious diseases that include malignant tumors. This study aimed to explore the clinical value of metagenomic next-generation sequencing (mNGS) for tumor detection in patients with suspected infections. Methods A multicenter, prospective case study involving patients diagnosed with suspected infections was conducted in four hospitals in Shanghai, China between July 2019 and January 2020. Based upon mNGS technologies and chromosomal copy number variation (CNV) analysis on abundant human genome, a new procedure named Onco-mNGS was established to simultaneously detect pathogens and malignant tumors in all of the collected samples from patients. Results Of 140 patients screened by Onco-mNGS testing, 115 patients were diagnosed with infections; 17 had obvious abnormal CNV signals indicating malignant tumors that were confirmed clinically. The positive percent agreement and negative percent agreement of mNGS testing compared to clinical diagnosis was 53.0% (61/115) and 60% (15/25), vs. 20.9% (24/115) and 96.0% (24/25), respectively, for conventional microbiological testing (both P <0.01). Klebsiella pneumoniae (14.8%, 9/61) was the most common pathogen detected by mNGS, followed by Escherichia coli (11.5%, 7/61) and viruses (11.5%, 7/61). The chromosomal abnormalities of the 17 cases included genome-wide variations and local variations of a certain chromosome. Five of 17 patients had a final confirmed with malignant tumors, including three lung adenocarcinomas and two hematological tumors; one patient was highly suspected to have lymphoma; and 11 patients had a prior history of malignant tumor. Conclusion This preliminary study demonstrates the feasibility and clinical value of using Onco-mNGS to simultaneously search for potential pathogens and malignant tumors in patients with suspected infections.
Collapse
Affiliation(s)
- Jiachun Su
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Xu Han
- Research and Development Department, MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,The National Clinical Research Center for Aging and Medicine, Huashan Hospital, Shanghai, China
| | - Wenchao Ding
- Research and Development Department, MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Ming Li
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiqin Wang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mi Tian
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiyuan Chen
- Department of Critical Care Medicine, Jing'an District Centre Hospital, Fudan University, Shanghai, China
| | - Binbin Xu
- Department of Neurosurgery, Putuo District People's Hospital, Tongji University, Shanghai, China
| | - Zhongqing Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinyi Yuan
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaohua Qin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Dongfang Lin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Ruilan Wang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ye Gong
- Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Liping Pan
- Department of Critical Care Medicine, Jing'an District Centre Hospital, Fudan University, Shanghai, China
| | - Jun Wang
- Research and Development Department, MatriDx Biotechnology Co., Ltd, Hangzhou, China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,The National Clinical Research Center for Aging and Medicine, Huashan Hospital, Shanghai, China
| |
Collapse
|
25
|
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
|
26
|
Zhan Z, Li CF, Liu J, Cao CS, Huang L. Metagenomic next-generation sequencing to diagnose atypical severe scrub typhus. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:556-557. [PMID: 34996709 DOI: 10.1016/j.jmii.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/23/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Zuan Zhan
- Emergency Department, The First Affiliated Hospital of Nanchang University, Jiangxi, China.
| | - Chun-Fan Li
- Emergency Department, The First Affiliated Hospital of Nanchang University, Jiangxi, China.
| | - Jian Liu
- Emergency Department, The First Affiliated Hospital of Nanchang University, Jiangxi, China.
| | - Chun-Shui Cao
- Emergency Department, The First Affiliated Hospital of Nanchang University, Jiangxi, China.
| | - Liang Huang
- Emergency Department, The First Affiliated Hospital of Nanchang University, Jiangxi, China.
| |
Collapse
|
27
|
Xu H, Hu X, Wang W, Chen H, Yu F, Zhang X, Zheng W, Han K. Clinical Application and Evaluation of Metagenomic Next-Generation Sequencing in Pulmonary Infection with Pleural Effusion. Infect Drug Resist 2022; 15:2813-2824. [PMID: 35677528 PMCID: PMC9167844 DOI: 10.2147/idr.s365757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/27/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Huifen Xu
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Xiaoman Hu
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Wenyu Wang
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Hong Chen
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Fangfei Yu
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Xiaofei Zhang
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Weili Zheng
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
| | - Kaiyu Han
- Department of Respiratory and Critical Medicine, the Second Affiliated Hospital of Harbin Medical University, Heilongjiang, People’s Republic of China
- Correspondence: Kaiyu Han, Tel +86-451-86605736, Email
| |
Collapse
|
28
|
Flurin L, Wolf M, Mutchler M, Daniels M, Wengenack N, Patel R. Targeted Metagenomic Sequencing-Based Approach Applied to 2,146 Tissue and Body Fluid Samples in Routine Clinical Practice. Clin Infect Dis 2022; 75:1800-1808. [PMID: 35362534 PMCID: PMC9662179 DOI: 10.1093/cid/ciac247] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The yield of next generation sequencing (NGS) added to a Sanger sequencing-based 16S ribosomal RNA (rRNA) gene PCR assay was evaluated in clinical practice for diagnosis of bacterial infection. METHODS PCR targeting the V1 to V3 regions of the 16S rRNA gene was performed, with amplified DNA submitted to Sanger sequencing and/or NGS (Illumina MiSeq), or reported as negative, depending on cycle threshold (Ct) value. 2,146 normally sterile tissues or body fluids were tested between August 2020 and March 2021. Clinical sensitivity was assessed in 579 subjects from whom clinical data was available. RESULTS Compared to Sanger sequencing alone (400 positive tests), positivity increased by 87% by adding NGS (347 added positive tests). Clinical sensitivity of the assay incorporating NGS was 53%, higher than culture (42%, p<0.001), with an impact on clinical decision-making in 14% of infected cases. Clinical sensitivity in the subgroup receiving antibiotics at sampling was 41% for culture and 63% for the sequencing assay (p<0.001). CONCLUSION Adding NGS to Sanger sequencing of the PCR-amplified 16S rRNA gene substantially improved test positivity. In the patient population studied, the assay was more sensitive than culture, and especially so in patients who had received antibiotic therapy.
Collapse
Affiliation(s)
- Laure Flurin
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA.,Department of Intensive Care, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Matthew Wolf
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Melissa Mutchler
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Matthew Daniels
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Nancy Wengenack
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Robin Patel
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA.,Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
29
|
Diagnostic performance of the metagenomic next-generation sequencing in lung biopsy tissues in patients suspected of having a local pulmonary infection. BMC Pulm Med 2022; 22:112. [PMID: 35351079 PMCID: PMC8962165 DOI: 10.1186/s12890-022-01912-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/23/2022] [Indexed: 12/15/2022] Open
Abstract
Purpose This study aims to evaluate the diagnostic application and performance of the metagenomic next-generation sequencing (mNGS) in patients suspected of local pulmonary infection by comparing it to the traditional pathogen detection methods in lung tissue specimens obtained by a computerized tomography-guided biopsy (CT-guided biopsy). Methods We retrospectively reviewed patients, admitted to the First Affiliated Hospital of Wenzhou Medical University, China from May 2018 to December 2020, who were suspected of local pulmonary infection. All cases received a CT-guided lung biopsy, tissue samples were sent both for conventional examinations (CE) and mNGS tests. The sensitivity and specificity of the two diagnostic approaches were compared. Results 106 patients enrolled, 76 patients were diagnosed with a pulmonary infection. Among 49 patients with identified pathogens, CE confirmed pathogenic infections in 32 cases. Mycobacterium spp. and fungi accounted for 37.5% (12/32) and 28.1% (9/32), respectively, with bacteria 34.4% (11/32). The mNGS examination detected extra pathogenic microorganisms in 22 patients that were consistent with the patients' clinical and radiographic pictures. The sensitivity of mNGS was 53.9% vs. 42.1% for the CE, while the specificity was 56.7% versus 96.7%. For detection rate, mNGS was significantly superior to CE in bacterial (96.3% vs. 40.7%, p < 0.05), and mixed infections (100% vs. 50%, p < 0.05), but inferior to CE in fungal (60% vs. 90%, p > 0.05) and Mycobacterium spp. infections (66.7% vs. 100%, p > 0.05) with no significant difference. Among 31 cases diagnosed with lung abscess, the diagnostic performance of the detection rate was 67.7% (21/31) in favour of mNGS compared to 29.0% (9/31) for CE (p < 0.05). Most polymicrobial infections were induced by anaerobic species that coexisted with Streptococcus constellatus. And Klebsiella pneumoniae was the most common isolated monomicrobial infection. Conclusions The most commonly detected causative pathogens for local pulmonary infections were bacteria, Mycobacterium spp. and fungi. Compared with the CE, the advantages of mNGS in the pathogens detection lie in the discovery of bacterial and mixed infections, as well as in the detection of lung abscess. Conversely, mNGS is not good enough to be recommendable for the detection of Mycobacterium spp. and fungi. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-022-01912-4.
Collapse
|
30
|
Sun W, Dong Z, Zhou Y, Xiong K, Liu H, Zhang Z, Fan L. Early Identification of Fungal and Mycobacterium Infections in Pulmonary Granulomas Using Metagenomic Next-Generation Sequencing on Formalin fixation and paraffin embedding tissue. Expert Rev Mol Diagn 2022; 22:461-468. [PMID: 35261303 DOI: 10.1080/14737159.2022.2052046] [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: 11/04/2022]
Abstract
BACKGROUND The purpose of the study is to assess the etiology detection ability of Metagenomic Next-Generation Sequencing (mNGS) on formalin fixation and paraffin embedding (FFPE) tissue from postoperative biopsy specimen. METHODS We prospectively enrolled specimens from patients undergone surgery biopsy due to undefinite diagnosis and pathologically indicated granulomatous lesions. FFPE tissues were tested by mNGS and histopathology. The etiology detection rate of mNGS was calculated and compared with histopathology, using the clinical diagnosis as the reference criteria. RESULTS Among the 69 cases eventually included, 41 (59.42%) were diagnosed as infectious granuloma. The overall fungi and mycobacteria etiology detection rate of mNGS in granuloma lesions was 87.80 % (36/41) . The mNGS increased detection rate by 68.29 % (28/41) compared with histopathology, the difference was statistically significant (χ2= 28.97, P 0.00).The detection rates of mNGS in fungal infections (12/12,100%) and in mycobacterium infections (22/27, 81.48%) were significant higher than those of histopathology (8/12, 66.67% and 0/27,0.00 %;both P 0.00). 2 (2/2.100%) cases of co-infection were detected at one time by mNGS. All mNGS-based clinical decisions were made within 2 days. CONCLUSIONS The mNGS could accurately and quickly detect fungi and mycobacteria on FFPE specimens from postoperative granuloma specimens and identify the pathogens to the species level. CLINICAL TRIALS REGISTRATION China Clinical Trial Registry ChiCTR2000035464.
Collapse
Affiliation(s)
- Wenwen Sun
- Department of Tuberculosis and Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai 200092, China
| | - Zhengwei Dong
- Department of Pathology, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai, China
| | - Yiming Zhou
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai, China
| | - Kunlong Xiong
- Department of Tuberculosis and Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai 200092, China
| | - Hongcheng Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai, China
| | | | - Lin Fan
- Department of Tuberculosis and Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai 200092, China
| |
Collapse
|
31
|
Wu M, Lan X, Lin S, Lai T, Lin W, Wu H. Synovial tuberculosis in wrist diagnosed based on metagenomic next-generation sequencing: A case report. EUR J INFLAMM 2022. [DOI: 10.1177/20587392221075507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Synovial tuberculosis in the wrist is a rare disease that is usually misdiagnosed at the early stage. In this case, we presented a 67-year-old male with wrist joint tuberculosis who presented repeated left wrist joint edema for more than 2 years. The patient received surgery twice. During the second surgery, the combination of metagenomic next-generation sequencing (mNGS) and pathological analysis contributed to the detection of Mycobacterium tuberculosis in lesion tissues. Conventional anti-tubercular therapy confirmed the diagnosis of synovial tuberculosis in the wrist joint. In conclusion, mNGS contributed to the rapid and accurate detection of tubercle bacillus.
Collapse
Affiliation(s)
- Meimei Wu
- Department of Digestive System, Fuzhou Second Hospital, Fuzhou, China
| | - Xianfeng Lan
- Department of Hand Surgery, Fuzhou Second Hospital, Fuzhou, China
| | - Shibei Lin
- Department of Hand Surgery, Fuzhou Second Hospital, Fuzhou, China
| | - Tian Lai
- Department of Hand Surgery, Fuzhou Second Hospital, Fuzhou, China
| | - Weiguo Lin
- Department of Digestive System, Fuzhou Second Hospital, Fuzhou, China
| | - Hao Wu
- Department of Hand Surgery, Fuzhou Second Hospital, Fuzhou, China
| |
Collapse
|
32
|
Fu ZF, Zhang HC, Zhang Y, Cui P, Zhou Y, Wang HY, Lin K, Zhou X, Wu J, Wu HL, Zhang WH, Ai JW. Evaluations of Clinical Utilization of Metagenomic Next-Generation Sequencing in Adults With Fever of Unknown Origin. Front Cell Infect Microbiol 2022; 11:745156. [PMID: 35127548 PMCID: PMC8813867 DOI: 10.3389/fcimb.2021.745156] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction The diagnosis of infection-caused fever of unknown origin (FUO) is still challenging, making it difficult for physicians to provide an early effective therapy. Therefore, a novel pathogen detection platform is needed. Metagenomic next-generation sequencing (mNGS) provides an unbiased, comprehensive technique for the sequence-based identification of pathogenic microbes, but the study of the diagnostic values of mNGS in FUO is still limited. Methods In a single-center retrospective cohort study, 175 FUO patients were enrolled, and clinical data were recorded and analyzed to compare mNGS with culture or traditional methods including as smears, serological tests, and nucleic acid amplification testing (NAAT) (traditional PCR, Xpert MTB/RIF, and Xpert MTB/RIF Ultra). Results The blood mNGS could increase the overall rate of new organisms detected in infection-caused FUO by roughly 22.9% and 19.79% in comparison to culture (22/96 vs. 0/96; OR, ∞; p = 0.000) and conventional methods (19/96 vs. 3/96; OR, 6.333; p = 0.001), respectively. Bloodstream infection was among the largest group of those identified, and the blood mNGS could have a 38% improvement in the diagnosis rate compared to culture (19/50 vs. 0/50; OR, ∞; p = 0.000) and 32.0% compared to conventional methods (16/50 vs. 3/50; OR, 5.333; p = 0.004). Among the non-blood samples in infection-caused FUO, we observed that the overall diagnostic performance of mNGS in infectious disease was better than that of conventional methods by 20% (9/45 vs. 2/45; OR, 4.5; p = 0.065), and expectedly, the use of non-blood mNGS in non-bloodstream infection increased the diagnostic rate by 26.2% (8/32 vs. 0/32; OR, ∞; p = 0.008). According to 175 patients’ clinical decision-making, we found that the use of blood mNGS as the first-line investigation could effectively increase 10.9% of diagnosis rate of FUO compared to culture, and the strategy that the mNGS of suspected parts as the second-line test could further benefit infectious patients, improving the diagnosis rate of concurrent infection by 66.7% and 12.5% in non-bloodstream infection, respectively. Conclusion The application of mNGS in the FUO had significantly higher diagnostic efficacy than culture or other conventional methods. In infection-caused FUO patients, application of blood mNGS as the first-line investigation and identification of samples from suspected infection sites as the second-line test could enhance the overall FUO diagnosis rate and serve as a promising optimized diagnostic protocol in the future.
Collapse
Affiliation(s)
- Zhang-fan Fu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Hao-cheng Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Peng Cui
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yang Zhou
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd., BGI-Shenzhen, Shenzhen, China
| | - Hong-yu Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ke Lin
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xian Zhou
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Hong-long Wu
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd., BGI-Shenzhen, Shenzhen, China
- BGI Wuhan Biotechnology, BGI-Shenzhen, Wuhan, China
| | - Wen-hong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing-wen Ai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Jingwen Ai,
| |
Collapse
|
33
|
|
34
|
Zhan L, Huang K, Xia W, Chen J, Wang L, Lu J, Wang J, Lin J, Wu W. The Diagnosis of Severe Fever with Thrombocytopenia Syndrome Using Metagenomic Next-Generation Sequencing: Case Report and Literature Review. Infect Drug Resist 2022; 15:83-89. [PMID: 35046673 PMCID: PMC8760998 DOI: 10.2147/idr.s345991] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
Background Severe fever with thrombocytopenia syndrome (SFTS) is an infectious disease caused by a bunyaviridae virus. Its main clinical manifestation is fever with thrombocytopenia, which may be accompanied by other clinical symptoms. Here, we report a patient diagnosed with SFTS using metagenomic next‑generation sequencing (mNGS). Case Presentation A 56-year-old female patient was hospitalized with intermittent diarrhea and fever. She visited a local clinic for treatment, but instead of improving, the symptoms progressed to unconsciousness. Diagnosis Using mNGS, we isolated the bunyaviridae virus and several other pathogens from the patient’s blood samples to confirm the diagnosis. Interventions The patient was treated with symptomatic and supportive therapy, including intravenous human γ-globulin (20 g/d), platelet transfusion, platelet elevation (subcutaneous injection of recombinant human thrombopoietin, 15,000 IU), white blood cell elevation (subcutaneous injection of recombinant human granulocyte colony-stimulating factor, 200 ug, qd); and antibiotic (cefoperazone sodium and tazobactam sodium, 2 g, q8h), antiviral (ganciclovir, 250 mg, q12h), and antifungal therapy (voriconazole for injection, 0.2 g, q12h). After ten days of treatment, the patient’s condition gradually improved. Conclusion Compared to traditional detection methods, mNGS has many advantages. It can quickly identify the pathogen when the patient’s clinical manifestations are complex and difficult to diagnose, resulting in the formulation of an effective treatment.
Collapse
Affiliation(s)
- Liying Zhan
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Kai Huang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Wenfang Xia
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Jingdi Chen
- Department of Orthopedics, The Airborne Military Hospital, Wuhan, Hubei, People’s Republic of China
| | - Lu Wang
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Jiaming Lu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Jing Wang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Jun Lin
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
| | - Wei Wu
- Department of Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, People’s Republic of China
- Correspondence: Wei Wu; Jun Lin Email ;
| |
Collapse
|
35
|
Miller S, Chiu C. The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis. Clin Chem 2021; 68:115-124. [PMID: 34969106 DOI: 10.1093/clinchem/hvab173] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) for pathogen detection is becoming increasingly available as a method to identify pathogens in cases of suspected infection. mNGS analyzes the nucleic acid content of patient samples with high-throughput sequencing technologies to detect and characterize microorganism DNA and/or RNA. This unbiased approach to organism detection enables diagnosis of a broad spectrum of infection types and can identify more potential pathogens than any single conventional test. This can lead to improved ability to diagnose patients, although there remains concern regarding contamination and detection of nonclinically significant organisms. CONTENT We describe the laboratory approach to mNGS testing and highlight multiple considerations that affect diagnostic performance. We also summarize recent literature investigating the diagnostic performance of mNGS assays for a variety of infection types and recommend further studies to evaluate the improvement in clinical outcomes and cost-effectiveness of mNGS testing. SUMMARY The majority of studies demonstrate that mNGS has sensitivity similar to specific PCR assays and will identify more potential pathogens than conventional methods. While many of these additional organism detections correlate with the expected pathogen spectrum based on patient presentations, there are relatively few formal studies demonstrating whether these are true-positive infections and benefits to clinical outcomes. Reduced specificity due to contamination and clinically nonsignificant organism detections remains a major concern, emphasizing the importance of careful interpretation of the organism pathogenicity and potential association with the clinical syndrome. Further research is needed to determine the possible improvement in clinical outcomes and cost-effectiveness of mNGS testing.
Collapse
Affiliation(s)
- Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
36
|
Tang Y, Zhao D, Wang S, Yi Q, Xia Y, Geng B. Diagnostic Value of Next-Generation Sequencing in Periprosthetic Joint Infection: A Systematic Review. Orthop Surg 2021; 14:190-198. [PMID: 34935279 PMCID: PMC8867422 DOI: 10.1111/os.13191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 11/11/2021] [Accepted: 11/19/2021] [Indexed: 01/03/2023] Open
Abstract
Next‐generation sequencing (NGS) has developed rapidly in the last decade and is emerging as a promising diagnostic tool for periprosthetic joint infection (PJI). However, its diagnostic value for PJI is still uncertain. This systematic review aimed to explore the diagnostic value of NGS for PJI and verify its accuracy for culture‐negative PJI patients. We conducted this systematic review in accordance with the Preferred Reporting Items for Systematic Reviews and Meta‐Analysis (PRISMA) guidelines. Medline, Embase, and Cochrane Library were searched to identify diagnostic technique studies evaluating the accuracy of NGS in the diagnosis of PJI. The diagnostic sensitivity, specificity, and positive and negative predictive values were estimated for each article. The detection rate of NGS for culture‐negative PJI patients or PJI patients with antibiotic administration history was also calculated. Of the 87 identified citations, nine studies met the inclusion criteria. The diagnostic sensitivities and specificities of NGS ranged from 63% to 96% and 73% to 100%, respectively. The positive and negative predictive values ranged from 71% to 100% and 74% to 95%, respectively. The detection rate of NGS for culture‐negative PJI patients in six studies was higher than 50% (range from 82% to 100%), while in three studies it was lower than 50% (range from 9% to 31%). Also, the detection rate of NGS for PJIs with antibiotic administration history ranged from 74.05% to 92.31%. In conclusion, this systematic review suggests that NGS may have the potential to be a new tool for the diagnosis of PJI and should be considered to be added to the portfolio of diagnostic procedures. Furthermore, NGS showed a favorable diagnostic accuracy for culture‐negative PJI patients or PJI patients with antibiotic administration history. However, due to the small sample sizes of studies and substantial heterogeneity among the included studies, more research is needed to confirm or disprove these findings.
Collapse
Affiliation(s)
- Yuchen Tang
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Dacheng Zhao
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Shenghong Wang
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Qiong Yi
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Yayi Xia
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Bin Geng
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| |
Collapse
|
37
|
Yang L, Song J, Wang Y, Feng J. Metagenomic Next-Generation Sequencing for Pulmonary Fungal Infection Diagnosis: Lung Biopsy versus Bronchoalveolar Lavage Fluid. Infect Drug Resist 2021; 14:4333-4359. [PMID: 34707378 PMCID: PMC8542593 DOI: 10.2147/idr.s333818] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/30/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose Metagenomic next-generation sequencing (mNGS) is widely used for pulmonary infection; nonetheless, the experience from its clinical use in diagnosing pulmonary fungal infections is sparse. This study aimed to compare mNGS results from lung biopsy and bronchoalveolar lavage fluid (BALF) and determine their clinical diagnostic efficacy. Patients and Methods A total of 106 patients with suspected pulmonary fungal infection from May 2018 to January 2020 were included in this retrospective study. All patients' lung biopsy and BALF specimens were collected through bronchoscopy. Overall, 45 (42.5%) patients had pulmonary fungal infection. The performance of lung biopsy and BALF used for mNGS in diagnosing pulmonary fungal infections and identifying pathogens was compared. Additionally, mNGS was compared with conventional tests (pathology, galactomannan test, and cultures) with respect to the diagnosis of pulmonary fungal infections. Results Lung biopsy-mNGS and BALF-mNGS exhibited no difference in terms of sensitivity (80.0% vs 84.4%, P=0.754) and specificity (91.8% vs 85.3%, P=0.39). Additionally, there was no difference in specificity between mNGS and conventional tests; however, the sensitivity of mNGS (lung biopsy, BALF) in diagnosing pulmonary fungal infections was significantly higher than that of conventional tests (conventional tests vs biopsy-mNGS: 44.4% vs 80.0%, P<0.05; conventional tests vs BALF-mNGS: 44.4% vs 84.4%, P<0.05). Among 32 patients with positive mNGS results for both biopsy and BALF specimens, 23 (71.9%) cases of consistency between the two tests for the detected fungi and nine (28.1%) cases of a partial match were identified. Receiver operating curve analysis revealed that the area under the curve for the combination of biopsy and BALF was significantly higher than that for BALF-mNGS (P=0.018). Conclusion We recommend biopsy-based or BALF-based mNGS for diagnosing pulmonary fungal infections because of their diagnostic advantages over conventional tests. The combination of biopsy and BALF for mNGS can be considered when higher diagnostic efficacy is required.
Collapse
Affiliation(s)
- Lei Yang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Junxiu Song
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Yubao Wang
- Institute of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, People's Republic of China
| | - Jing Feng
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| |
Collapse
|
38
|
Diagnostic Accuracy of Metagenomic Next-Generation Sequencing in Sputum-Scarce or Smear-Negative Cases with Suspected Pulmonary Tuberculosis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9970817. [PMID: 34527747 PMCID: PMC8437628 DOI: 10.1155/2021/9970817] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/09/2021] [Accepted: 08/25/2021] [Indexed: 12/28/2022]
Abstract
Objective To investigate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) samples or lung biopsy specimens from which suspected pulmonary tuberculosis (PTB) patients have no sputum or negative smear. Materials and Methods Sputum-scarce or smear-negative cases with suspected PTB (n = 107) were analyzed from January 2018 to June 2020. We collected BALF or lung tissue biopsy samples with these cases of suspected TB during hospitalization. The diagnostic accuracy of mNGS for these samples was compared with those of conventional tests or the T-SPOT.TB assay. Results 46 cases of PTB patients and 61 cases of non-PTB patients were finally enrolled and analyzed. mNGS exhibited a sensitivity of 89.13%, which was higher than conventional tests (67.39%) but equivalent to those of the T-SPOT.TB assay alone (76.09%) or T-SPOT.TB assay in combination with conventional tests (91.30%). The specificity of mNGS was 98.36%, similar to conventional tests (95.08%) but significantly higher than those of the T-SPOT.TB assay alone (65.57%) or the T-SPOT.TB assay in combination with conventional tests (63.93%). There was no significant difference in the diagnostic accuracy of mNGS in BALF samples and lung biopsy tissue specimens. Conclusion Our findings demonstrate that mNGS could offer improved detection of Mycobacterium tuberculosis in BALF or lung tissue biopsy samples in sputum-scarce or smear-negative cases with suspected PTB.
Collapse
|
39
|
Tang W, Zhang Y, Luo C, Zhou L, Zhang Z, Tang X, Zhao X, An Y. Clinical Application of Metagenomic Next-Generation Sequencing for Suspected Infections in Patients With Primary Immunodeficiency Disease. Front Immunol 2021; 12:696403. [PMID: 34484193 PMCID: PMC8414648 DOI: 10.3389/fimmu.2021.696403] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/28/2021] [Indexed: 01/22/2023] Open
Abstract
Background Infections are the major cause of morbidity and mortality in patients with primary immunodeficiency disease (PID). Timely and accurate microbiological diagnosis is particularly important in these patients. Metagenomic next-generation sequencing (mNGS) has been used for pathogen detection recently. However, few reports describe the use of mNGS for pathogen identification in patients with PID. Objective To evaluate the utility of mNGS for detecting pathogens in patients with PID, and to compare it with conventional microbiological tests (CMT). Methods This single center retrospective study investigated the diagnostic performance of mNGS for pathogens detection in PID patients and compared it with CMT. Sixteen PID patients with suspected infection were enrolled, and medical records were analyzed to extract detailed clinical characteristics such as gene variation, immune status, microbial distribution, time-consuming of mNGS and CMT, treatment, and outcomes. Results mNGS identified pathogenic microbe in 93.75% samples, compared to 31.25% for culture and 68.75% for conventional methods, and detected an extra 18 pathogenic microorganisms including rare opportunistic pathogens and Mycobacterium tuberculosis. Pathogen identification by mNGS required 48 hours, compared with bacterial culture for 3-7 days and even longer for fungus and Mycobacterium tuberculosis culture. Conclusions mNGS has marked advantages over conventional methods for pathogenic diagnosis, particularly opportunistic pathogens and mixed infections, in patients with PID. This method might enable clinicians to make more timely and targeted therapeutic decisions, thereby improving the prognosis of these patients.
Collapse
Affiliation(s)
- Wenjing Tang
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yu Zhang
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Chong Luo
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Lina Zhou
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zhiyong Zhang
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Tang
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaodong Zhao
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yunfei An
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| |
Collapse
|
40
|
Li N, Li S, Tan W, Wang H, Xu H, Wang D. Metagenomic next-generation sequencing in the family outbreak of psittacosis: the first reported family outbreak of psittacosis in China under COVID-19. Emerg Microbes Infect 2021; 10:1418-1428. [PMID: 34176434 PMCID: PMC8284143 DOI: 10.1080/22221751.2021.1948358] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chlamydia psittaci infection in humans, also known as psittacosis, is usually believed to be an uncommon disease which mainly presents as community-acquired pneumonia (CAP). It is usually sporadic, but outbreaks of infection may occasionally occur. In outbreaks, diagnosis and investigations were usually hampered by the non-specificity of laboratory testing methods to identify C. psittaci. In this study, we use metagenomic next-generation sequencing (mNGS) in the diagnosis of a family outbreak of psittacosis under COVID-19. Three members of an extended family of 6 persons developed psittacosis with pneumonia and hepatic involvement with common symptoms of fever and weakness. Two newly purchased pet parrots, which had died successively, were probably the primary source of infection. Imagings show lung consolidations and infiltrates, which are difficult to be differentiated from CAP caused by other common pathogens. mNGS rapidly identified the infecting agent as C. psittaci within 48 h. The results of this work suggest that there are not characteristic clinical manifestations and imagings of psittacosis pneumonia which can differentiate from CAP caused by other pathogens. The use of mNGS can improve accuracy and reduce the delay in the diagnosis of psittacosis especially during the outbreak, which can shorten the course of the disease control. Family outbreak under COVID-19 may be related to the familial aggregation due to the epidemic. To our knowledge, this is the first reported family outbreak of psittacosis in China, and the first reported psittacosis outbreak identified by the method of mNGS in the world.
Collapse
Affiliation(s)
- Na Li
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Shengjin Li
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Wanmei Tan
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Hanghang Wang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Huan Xu
- Vision Medicals Center for Infection Diseases, Guangzhou, People's Republic of China
| | - Daoxing Wang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| |
Collapse
|
41
|
Ye Y, Yang N, Zhou J, Qian G, Chu J. Case Report: Metagenomic Next-Generation Sequencing in Diagnosis of Disseminated Tuberculosis of an Immunocompetent Patient. Front Med (Lausanne) 2021; 8:687984. [PMID: 34322503 PMCID: PMC8310911 DOI: 10.3389/fmed.2021.687984] [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: 03/30/2021] [Accepted: 06/14/2021] [Indexed: 01/05/2023] Open
Abstract
Disseminated tuberculosis (TB) is a rare disease and mainly occurs in immunodeficient patients. It is marked by hematogenous or lymphatic dissemination of Mycobacterium tuberculosis, causing tuberculous infection involving any organ system. Here, we report a case of disseminated TB involving lung, liver, spine, mediastinum, and prostate in an immunocompetent man. The present patient found a hepatic mass without any symptom during health examination. In the next 2 years, further examinations revealed multiple lesions in the lung, mediastinum, spine, and prostate. Imaging examinations, such as contrast-enhanced abdominal CT, F-18 FDG-PET/CT, and radionuclide bone scan, suggested the diagnosis of malignancy or metastatic tumor. Furthermore, histopathological results of the biopsies of the hepatic mass, mediastinal mass, and prostatic mass demonstrated granulomatous inflammation. Therefore, metagenomic next-generation sequencing (mNGS) was utilized to confirm the diagnosis. Mycobacterium tuberculosis complex was simultaneously detected in the spinal surgical resection specimens and bronchoalveolar lavage fluid (BALF), indicating the diagnosis of disseminated TB. mNGS is an emerging molecular diagnostic technology, and its application in disseminated TB has been rarely reported. We highlight that disseminated TB should be considered even in an immunocompetent patient, and mNGS can be performed when the diagnosis is difficult.
Collapse
Affiliation(s)
- Yuanting Ye
- School of Medicine, Ningbo University, Ningbo, China.,Department of General Practice, Ningbo First Hospital, Ningbo, China
| | - Naibin Yang
- Department of Infectious Disease, Ningbo First Hospital, Ningbo, China
| | - Jingying Zhou
- Department of Hematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guoqing Qian
- Department of Infectious Disease, Ningbo First Hospital, Ningbo, China
| | - Jinguo Chu
- Department of General Practice, Ningbo First Hospital, Ningbo, China
| |
Collapse
|
42
|
Ge M, Gan M, Yan K, Xiao F, Yang L, Wu B, Xiao M, Ba Y, Zhang R, Wang J, Cheng G, Wang L, Cao Y, Zhou W, Hu L. Combining Metagenomic Sequencing With Whole Exome Sequencing to Optimize Clinical Strategies in Neonates With a Suspected Central Nervous System Infection. Front Cell Infect Microbiol 2021; 11:671109. [PMID: 34222042 PMCID: PMC8253254 DOI: 10.3389/fcimb.2021.671109] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/27/2021] [Indexed: 12/02/2022] Open
Abstract
Objectives Central nervous system (CNS) infection has a high incidence and mortality in neonates, but conventional tests are time-consuming and have a low sensitivity. Some rare genetic diseases may have some similar clinical manifestations as CNS infection. Therefore, we aimed to evaluate the performance of metagenomic next-generation sequencing (mNGS) in diagnosing neonatal CNS infection and to explore the etiology of neonatal suspected CNS infection by combining mNGS with whole exome sequencing (WES). Methods We prospectively enrolled neonates with a suspected CNS infection who were admitted to the neonatal intensive care unit(NICU) from September 1, 2019, to May 31, 2020. Cerebrospinal fluid (CSF) samples collected from all patients were tested by using conventional methods and mNGS. For patients with a confirmed CNS infection and patients with an unclear clinical diagnosis, WES was performed on blood samples. Results Eighty-eight neonatal patients were enrolled, and 101 CSF samples were collected. Fourty-three blood samples were collected for WES. mNGS showed a sample diagnostic yield of 19.8% (20/101) compared to 4.95% (5/101) for the conventional methods. In the empirical treatment group, the detection rate of mNGS was significantly higher than that of conventional methods [27% vs. 6.3%, p=0.002]. Among the 88 patients, 15 patients were etiologically diagnosed by mNGS alone, five patients were etiologically identified by WES alone, and one patient was diagnosed by both mNGS and WES. Twelve of 13 diagnoses based solely on mNGS had a likely clinical effect. Six patients diagnosed by WES also experienced clinical effect. Conclusions For patients with a suspected CNS infections, mNGS combined with WES might significantly improve the diagnostic rate of the etiology and effectively guide clinical strategies.
Collapse
Affiliation(s)
- Mengmeng Ge
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Mingyu Gan
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Kai Yan
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Feifan Xiao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Lin Yang
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Shanghai, China
| | - Mili Xiao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Yin Ba
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Rong Zhang
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Jin Wang
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Guoqiang Cheng
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Laishuan Wang
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Yun Cao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Wenhao Zhou
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China.,Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| |
Collapse
|
43
|
Jin Y, Wang Z, Zhu C, Yang Q, Lu Y, Yu X, Hong B, Wang X, Zhang Y. Case Report: Proven Diagnosis of Culture-Negative Chronic Disseminated Candidiasis in a Patient Suffering From Hematological Malignancy: Combined Application of mNGS and CFW Staining. Front Med (Lausanne) 2021; 8:627166. [PMID: 33718404 PMCID: PMC7943471 DOI: 10.3389/fmed.2021.627166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/20/2021] [Indexed: 12/03/2022] Open
Abstract
Chronic disseminated candidiasis (CDC) is a severe complication with high morbidity and mortality in patients with hematological malignancies who have undergone chemotherapy. Blood or sterile liver biopsy cultures are negative due to recurrent empirical antifungal therapy. With the escalating resistance to azole-based antifungal drugs in infection by Candida species, pathogen identification is becoming increasingly important for determining definitive diagnosis and treatment strategy. In this case report, we present, for the first time, diagnostic confirmation of a culture-negative CDC case with Candida tropicalis infection using a combination of metagenomics next-generation sequencing and calcofluor white staining.
Collapse
Affiliation(s)
- Yanqi Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhouhan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Chunxia Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Qing Yang
- Laboratory Department, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yingfeng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaopeng Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Bao Hong
- Department of Infectious Diseases of Haining Campus, The First Affiliated Hospital, College of Medicine, Zhejiang University, Haining, China
| | - Xiaojing Wang
- Department of Infectious Diseases of Haining Campus, The First Affiliated Hospital, College of Medicine, Zhejiang University, Haining, China
| | - Yimin Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Infectious Diseases of Haining Campus, The First Affiliated Hospital, College of Medicine, Zhejiang University, Haining, China
| |
Collapse
|
44
|
Qian YY, Wang HY, Zhou Y, Zhang HC, Zhu YM, Zhou X, Ying Y, Cui P, Wu HL, Zhang WH, Jin JL, Ai JW. Improving Pulmonary Infection Diagnosis with Metagenomic Next Generation Sequencing. Front Cell Infect Microbiol 2021; 10:567615. [PMID: 33585263 PMCID: PMC7874146 DOI: 10.3389/fcimb.2020.567615] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 12/04/2020] [Indexed: 02/03/2023] Open
Abstract
Pulmonary infections are among the most common and important infectious diseases due to their high morbidity and mortality, especially in older and immunocompromised individuals. However, due to the limitations in sensitivity and the long turn-around time (TAT) of conventional diagnostic methods, pathogen detection and identification methods for pulmonary infection with greater diagnostic efficiency are urgently needed. In recent years, unbiased metagenomic next generation sequencing (mNGS) has been widely used to detect different types of infectious pathogens, and is especially useful for the detection of rare and newly emergent pathogens, showing better diagnostic performance than traditional methods. There has been limited research exploring the application of mNGS for the diagnosis of pulmonary infections. In this study we evaluated the diagnostic efficiency and clinical impact of mNGS on pulmonary infections. A total of 100 respiratory samples were collected from patients diagnosed with pulmonary infection in Shanghai, China. Conventional methods, including culture and standard polymerase chain reaction (PCR) panel analysis for respiratory tract viruses, and mNGS were used for the pathogen detection in respiratory samples. The difference in the diagnostic yield between conventional methods and mNGS demonstrated that mNGS had higher sensitivity than traditional culture for the detection of pathogenic bacteria and fungi (95% vs 54%; p<0.001). Although mNGS had lower sensitivity than PCR for diagnosing viral infections, it identified 14 viral species that were not detected using conventional methods, including multiple subtypes of human herpesvirus. mNGS detected viruses with a genome coverage >95% and a sequencing depth >100× and provided reliable phylogenetic and epidemiological information. mNGS offered extra benefits, including a shorter TAT. As a complementary approach to conventional methods, mNGS could help improving the identification of respiratory infection agents. We recommend the timely use of mNGS when infection of mixed or rare pathogens is suspected, especially in immunocompromised individuals and or individuals with severe conditions that require urgent treatment.
Collapse
Affiliation(s)
- Yi-Yi Qian
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Hong-Yu Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yang Zhou
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Hao-Cheng Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yi-Min Zhu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xian Zhou
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yue Ying
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Peng Cui
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Hong-Long Wu
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen, Shenzhen, China.,BGI Wuhan Biotechnology, BGI-Shenzhen, Wuhan, China
| | - Wen-Hong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jia-Lin Jin
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing-Wen Ai
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
45
|
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
|
46
|
Qian L, Shi Y, Li F, Wang Y, Ma M, Zhang Y, Shao YW, Zheng G, Zhang G. Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of External Ventricular and Lumbar Drainage-Associated Ventriculitis and Meningitis. Front Microbiol 2021; 11:596175. [PMID: 33381092 PMCID: PMC7767851 DOI: 10.3389/fmicb.2020.596175] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/13/2020] [Indexed: 12/20/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has become a widely used technology that can accurately detect individual pathogens. This prospective study was performed between February 2019 and September 2019 in one of the largest clinical neurosurgery centers in China. The study aimed to evaluate the performance of mNGS on cerebrospinal fluid (CSF) from neurosurgical patients for the diagnosis of external ventricular and lumbar drainage (EVD/LD)-associated ventriculitis and meningitis (VM). We collected CSF specimens from neurosurgical patients with EVD/LD for more than 24 h to perform conventional microbiological studies and mNGS analyses in a pairwise manner. We also investigated the usefulness of mNGS of CSF for the diagnosis of EVD/LD-associated VM. In total, 102 patients were enrolled in this study and divided into three groups, including confirmed VM (cVM) (39), suspected VM (sVM) (49), and non-VM (nVM) (14) groups. Of all the patients, mNGS detected 21 Gram-positive bacteria, 20 Gram-negative bacteria, and five fungi. The three primary bacteria detected were Staphylococcus epidermidis (9), Acinetobacter baumannii (5), and Staphylococcus aureus (3). The mNGS-positive coincidence rate of confirmed EVD/LD-associated VM was 61.54% (24/39), and the negative coincidence rate of the nVM group was 100% (14/14). Of 15 VM pathogens not identified by mNGS in the cVM group, eight were negative with mNGS and seven were inconsistent with the conventional microbiological identification results. In addition, mNGS identified pathogens in 22 cases that were negative using conventional methods; of them, 10 patients received a favorable clinical treatment; thus, showing the benefit of mNGS-guided therapy.
Collapse
Affiliation(s)
- Lingye Qian
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yijun Shi
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fangqiang Li
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yufei Wang
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Miao Ma
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanfang Zhang
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yang W Shao
- Nanjing Geneseeq Technology Inc., Nanjing, China.,School of Public Health, Nanjing Medical University, Nanjing, China
| | - Guanghui Zheng
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guojun Zhang
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
47
|
Clinical efficacy of metagenomic next-generation sequencing for rapid detection of Mycobacterium tuberculosis in smear-negative extrapulmonary specimens in a high tuberculosis burden area. Int J Infect Dis 2020; 103:91-96. [PMID: 33227518 DOI: 10.1016/j.ijid.2020.11.165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE The aim of this study was to assess the clinical utility of metagenomic next-generation sequencing (mNGS) on smear-negative extrapulmonary specimens collected in China. METHODS Specimens were tested by mNGS and other routine tests for tuberculosis (TB). The diagnostic accuracy of mNGS was calculated and compared with the final clinical diagnosis. RESULTS The sensitivity of mNGS was found to be significantly higher than the sensitivities of the other routine TB tests. Receiver operating characteristic curve analysis showed that mNGS achieved the highest area under the curve (AUC) value of 0.79. The mNGS positive rate was highest for tuberculous meningitis. All non-tuberculous extrapulmonary pathogens were directly and simultaneously detected. CONCLUSIONS mNGS appeared to be superior to all previous etiological tests for TB on smear-negative extrapulmonary specimens and could identify all possible pathogens at once within 48 h.
Collapse
|
48
|
Wu H, Wei J, Yu D. Application of NGS in Diagnosis of Tuberculous Pleurisy with Multiple Negative Tests: A Case Report. Infect Drug Resist 2020; 13:3543-3550. [PMID: 33116673 PMCID: PMC7553599 DOI: 10.2147/idr.s269779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022] Open
Abstract
Background Tuberculous pleurisy is inflammation caused by direct infection of Mycobacterium tuberculosis (MTB) and/or delayed allergic reaction of the pleura to MTB thallus components. The diagnosis of tuberculous pleurisy is mainly confirmed by bacterial culture, smear staining or histopathology, but has some clinical limitations. Next-generation sequencing (NGS), as a new diagnostic technology, has good application prospects in the diagnosis of tuberculous pleurisy. Case Presentation A patient admitted with right pleural effusion and pneumonia was actively treated with anti-infection, anti-inflammatory and symptomatic support while various etiological tests of right pleural effusion were improved. However, all the etiological tests for MTB infection were negative. At this time, the patient’s condition worsened and pleural effusion also appeared on the left side. In order to clarify the cause of the disease as soon as possible and prevent the disease from worsening again, the left and right pleural effusions of the patient were sent for NGS testing. The test results suggested MTB infection, which finally clarified the diagnosis of tuberculous pleurisy, and the next treatment plan of the patient was timely adjusted. Conclusion NGS is instructive in the diagnosis of tuberculous pleurisy when various conventional tests and imaging methods fail.
Collapse
Affiliation(s)
- Honglin Wu
- Department of Respiratory Medicine, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China.,Department of Gastroenterology, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China
| | - Jiahui Wei
- Department of Respiratory Medicine, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China
| | - Dujuan Yu
- Department of Respiratory Medicine, China-Japan Union Hospital of Jilin University, Changchun 130033, People's Republic of China
| |
Collapse
|
49
|
He R, Wang Q, Zhang F, Tang J, Shen H, Zhang X. Metagenomic sequencing in the management of fungal periprosthetic joint infection. J Infect 2020; 81:816-846. [PMID: 32956727 DOI: 10.1016/j.jinf.2020.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Renke He
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's, Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China
| | - Qiaojie Wang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's, Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China
| | - Feiyang Zhang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's, Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China
| | - Jin Tang
- Department of Clinical Laboratory, Shanghai Jiao Tong University Affiliated Sixth, People's Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China
| | - Hao Shen
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's, Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China.
| | - Xianlong Zhang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's, Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China.
| |
Collapse
|
50
|
Zhang H, Zhang Y, Wu J, Li Y, Zhou X, Li X, Chen H, Guo M, Chen S, Sun F, Mao R, Qiu C, Zhu Z, Ai J, Zhang W. Risks and features of secondary infections in severe and critical ill COVID-19 patients. Emerg Microbes Infect 2020; 9:1958-1964. [PMID: 32815458 PMCID: PMC8284966 DOI: 10.1080/22221751.2020.1812437] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Objectives Severe or critical COVID-19 is associated with intensive care unit admission, increased secondary infection rate, and would lead to significant worsened prognosis. Risks and characteristics relating to secondary infections in severe COVID-19 have not been described. Methods Severe and critical COVID-19 patients from Shanghai were included. We collected lower respiratory, urine, catheters, and blood samples according to clinical necessity and culture and mNGS were performed. Clinical and laboratory data were archived. Results We found 57.89% (22/38) patients developed secondary infections. The patient receiving invasive mechanical ventilation or in critical state has a higher chance of secondary infections (P<0.0001). The most common infections were respiratory, blood-stream and urinary infections, and in respiratory infections, the most detected pathogens were gram-negative bacteria (26, 50.00%), following by gram-positive bacteria (14, 26.92%), virus (6, 11.54%), fungi (4, 7.69%), and others (2, 3.85%). Respiratory Infection rate post high flow, tracheal intubation, and tracheotomy were 12.90% (4/31), 30.43% (7/23), and 92.31% (12/13) respectively. Secondary infections would lead to lower discharge rate and higher mortality rate. Conclusion Our study originally illustrated secondary infection proportion in severe and critical COVID-19 patients. Culture accompanied with metagenomics sequencing increased pathogen diagnostic rate. Secondary infections risks increased after receiving invasive respiratory ventilations and intravascular devices, and would lead to a lower discharge rate and a higher mortality rate.
Collapse
Affiliation(s)
- Haocheng Zhang
- Department of Infectious Disease, Huashan Hospital affiliated to Fudan University, Shanghai, People's Republic of China
| | - Yi Zhang
- Department of Infectious Disease, Huashan Hospital affiliated to Fudan University, Shanghai, People's Republic of China
| | - Jing Wu
- Department of Infectious Disease, Huashan Hospital affiliated to Fudan University, Shanghai, People's Republic of China
| | - Yang Li
- Department of Infectious Disease, Huashan Hospital affiliated to Fudan University, Shanghai, People's Republic of China
| | - Xian Zhou
- Department of Infectious Disease, Huashan Hospital affiliated to Fudan University, Shanghai, People's Republic of China
| | - Xin Li
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, People's Republic of China
| | - Haili Chen
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, People's Republic of China
| | - Mingquan Guo
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, People's Republic of China
| | - Shu Chen
- Department of Infectious Disease, Huashan Hospital affiliated to Fudan University, Shanghai, People's Republic of China
| | - Feng Sun
- Department of Infectious Disease, Huashan Hospital affiliated to Fudan University, Shanghai, People's Republic of China
| | - Richeng Mao
- Department of Infectious Disease, Huashan Hospital affiliated to Fudan University, Shanghai, People's Republic of China
| | - Chao Qiu
- Department of Infectious Disease, Huashan Hospital affiliated to Fudan University, Shanghai, People's Republic of China
| | - Zhaoqin Zhu
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Shanghai, People's Republic of China
| | - Jingwen Ai
- Department of Infectious Disease, Huashan Hospital affiliated to Fudan University, Shanghai, People's Republic of China
| | - Wenhong Zhang
- Department of Infectious Disease, Huashan Hospital affiliated to Fudan University, Shanghai, People's Republic of China
| |
Collapse
|