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Zhang J, Hou XY, Wang JY, Lu B. Case report: Cutaneous anthrax diagnosed using mNGS of a formalin-fixed paraffin-embedded tissue sample. Front Cell Infect Microbiol 2024; 14:1329235. [PMID: 38638828 PMCID: PMC11024221 DOI: 10.3389/fcimb.2024.1329235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/11/2024] [Indexed: 04/20/2024] Open
Abstract
The metagenomic next-generation sequencing (mNGS) method is preferred for genotyping useful for the identification of organisms, illumination of metabolic pathways, and determination of microbiota. It can accurately obtain all the nucleic acid information in the test sample. Anthrax is one of the most important zoonotic diseases, infecting mainly herbivores and occasionally humans. The disease has four typical clinical forms, cutaneous, gastrointestinal, inhalation, and injection, all of which may result in sepsis or meningitis, with cutaneous being the most common form. Here, we report a case of cutaneous anthrax diagnosed by mNGS in a butcher. Histopathology of a skin biopsy revealed PAS-positive bacilli. Formalin-fixed paraffin-embedded (FFPE) tissue sample was confirmed the diagnosis of anthrax by mNGS. He was cured with intravenous penicillin. To our knowledge, this is the first case of cutaneous anthrax diagnosed by mNGS using FFPE tissue. mNGS is useful for identifying pathogens that are difficult to diagnose with conventional methods, and FFPE samples are simple to manage. Compared with traditional bacterial culture, which is difficult to cultivate and takes a long time, mNGS can quickly and accurately help us diagnose anthrax, so that anthrax can be controlled in a timely manner and prevent the outbreak of epidemic events.
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Affiliation(s)
- Jin Zhang
- Department of Clinical Medicine, Jining Medical University, Jining, Shandong, China
- Department of Dermatology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Xin-Yi Hou
- Department of Clinical Medicine, Jining Medical University, Jining, Shandong, China
- Department of Dermatology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Jing-Yu Wang
- Department of Clinical Medicine, Jining Medical University, Jining, Shandong, China
- Department of Dermatology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Bin Lu
- Department of Dermatology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
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Zhao M, Zhang Y, Chen L, Yan X, Xu T, Fu M, Han Y, Zhang Y, Zhang B, Cao J, Lin J, Shen D, Li S, Zhu C, Zhao W. Nanopore sequencing of infectious fluid is a promising supplement for gold-standard culture in real-world clinical scenario. Front Cell Infect Microbiol 2024; 14:1330788. [PMID: 38352054 PMCID: PMC10861792 DOI: 10.3389/fcimb.2024.1330788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Infectious diseases are major causes of morbidity and mortality worldwide, necessitating the rapid identification and accurate diagnosis of pathogens. While unbiased metagenomic next-generation sequencing (mNGS) has been extensively utilized in clinical pathogen identification and scientific microbiome detection, there is limited research about the application of nanopore platform-based mNGS in the diagnostic performance of various infectious fluid samples. Methods In this study, we collected 297 suspected infectious fluids from 10 clinical centers and detected them with conventional microbiology culture and nanopore platform-based mNGS. The objective was to assess detective and diagnostic performance of nanopore-sequencing technology (NST) in real-world scenarios. Results Combined with gold-standard culture and clinical adjudication, nanopore sequencing demonstrated nearly 100% positive predictive agreements in microbial-colonized sites, such as the respiratory and urinary tracts. For samples collected from initially sterile body sites, the detected microorganisms were highly suspected pathogens, and the negative predictive agreements were relatively higher than those in the microbial-colonized sites, particularly with 100% in abscess and 95.7% in cerebrospinal fluid. Furthermore, consistent performance was also observed in the identification of antimicrobial resistance genes and drug susceptibility testing of pathogenic strains of Escherichia coli, Staphylococcus aureus, and Acinetobacter baumannii. Discussion Rapid NST is a promising clinical tool to supplement gold-standard culture, and it has the potential improve patient prognosis and facilitate clinical treatment of infectious diseases.
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Affiliation(s)
- Manna Zhao
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yongyang Zhang
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Li Chen
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xuebing Yan
- Department of Infectious Disease, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Tianmin Xu
- Department of Infectious Diseases, The Third People’s Hospital of Changzhou, Changzhou, Jiangsu, China
| | - Maoying Fu
- Infectious Diseases Department, Kunshan First People’s Hospital, Kunshan, Jiangsu, China
| | - Yangguang Han
- Department of Infectious Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ying Zhang
- Department of Infection Medicine, The Fifth People’s Hospital of Wuxi, Affiliated Wuxi Fifth Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Bin Zhang
- Department of Infectious Diseases, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Juan Cao
- Emergency Department, Shanghai Shibei Hospital, Shanghai, China
| | - Jing Lin
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Dan Shen
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Shuo Li
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
- Medical Department, Nanjing Dian Diagnostics Group Co., Ltd., Nanjing, Jiangsu, China
| | - Chuanlong Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weifeng Zhao
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Jiang J, Li Y, Wang Q, Zeng H, Yang W, Wu Y, Peng W, Pan P, Hu C, Deng P. Clinical implications of trichomonads detected in bronchoalveolar fluid by metagenomic next-generation sequencing: a multicenter retrospective study. Front Cell Infect Microbiol 2024; 14:1289231. [PMID: 38318165 PMCID: PMC10839053 DOI: 10.3389/fcimb.2024.1289231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Background Pulmonary trichomoniasis is considered a neglected disease due to failures in recognizing it, stemming from insensitive microbial methods and a lack of specific clinical features. This study aims to analyze the clinical implications of trichomonads detected in bronchoalveolar lavage fluid (BALF) by metagenomic next-generation sequencing (mNGS). Methods This multicenter retrospective study included patients diagnosed with pneumonia, admitted to three tertiary hospitals in China from July 2018 to September 2022, with trichomonads detected in BALF through mNGS. The analysis covered demographics, comorbidities, symptoms, laboratory findings, mNGS results, clinical treatment, and outcomes of these patients. Results A total of 17 patients were enrolled, comprising 14 males and 3 females. Trichomonas tenax and Trichomonas vaginalis were detected by mNGS in BALF samples of 15 and 2 patients, respectively. Patients were categorized into two groups based on the presence of risk factors for trichomonad infection, including immunocompromised conditions, uncontrolled diabetes mellitus, oral/periodontal diseases, and aspiration. Among 11 patients with risk factors (Case 1-11), 4 received nitromidazoles as part of comprehensive treatment, achieving a 100% treatment success rate. The remaining 7 patients, who did not receive nitromidazoles, had only one achieving relief after broad-spectrum antimicrobial therapy, resulting in a 14.3% treatment success rate. For the 6 patients without any risk factors for trichomonad infection (Case 12-17), none received nitromidazoles during hospitalization. However, 4 out of these 6 patients (66.7%) eventually recovered. Conclusion mNGS proves to be an efficient tool for detecting trichomonads in BALF samples. Comprehensive analysis of clinical features and laboratory indicators is essential to distinguish between infection and colonization of trichomonads. Pulmonary trichomoniasis should not be overlooked when trichomonads are detected in BALF from patients with risk factors.
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Affiliation(s)
- Juan Jiang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, China
| | - Yuanyuan Li
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, China
| | - Qiong Wang
- Department of Respiratory and Critical Care Medicine, Zhuzhou Second Hospital, Zhuzhou, China
| | - Huihui Zeng
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Yang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, China
| | - Yanhao Wu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, China
| | - Wenzhong Peng
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, China
| | - Pinhua Pan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, China
| | - Chengping Hu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, China
| | - Pengbo Deng
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, China
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Zhou T, Zheng Y, Zhang H, Liu Y. A case report of diagnosis of cat-scratch disease using metagenomic next-generation sequencing. Front Cell Infect Microbiol 2024; 13:1322651. [PMID: 38287977 PMCID: PMC10822884 DOI: 10.3389/fcimb.2023.1322651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/12/2023] [Indexed: 01/31/2024] Open
Abstract
Cat-scratch disease (CSD) is an anthropozoonotic infection caused by Bartonella henselae, and it is one of the most common causes of lymph node infections in children and adolescents. B. henselae, belonging to the genus Bartonella, is a common human pathogen of human beings. CSD commonly develops as a result of cat scratches and bites or when injured skin comes into contact with cat saliva. The manifestation of CSD clinically differs for each patient based on their immune system. Individuals who have healthy immune systems generally manifest minimal clinical symptoms and do not necessitate any form of treatment. However, patients who have hypo-immunity require prompt medical attention due to the potential manifestation of severe symptoms that affect multiple systems of the body. Long latency and atypical clinical manifestations are characteristics of CSD. Bartonella isolation and identification are challenging procedures that require specialized equipment. There is no gold standard method for CSD diagnosis, and misdiagnosis and missed diagnosis rates are typically high. We present the case of a middle-aged male patient who developed fever, chills, anal distension, dizziness, and muscle pain for 10 days. The patient had a documented history of cat bites 1 month prior to the onset of symptoms. Following admission, he underwent an examination to determine superficial lymphadenopathy and hypoimmunity. Additionally, he had a fever during the disease. As the patient refused a needle biopsy of lymph nodes, metagenomic next-generation sequencing (mNGS) was employed and B. henselae was detected in the peripheral blood. The patient was diagnosed with CSD and treated with a combination of azithromycin and doxycycline. The fever symptoms were alleviated, and the patient was ultimately discharged. As a result of this case, we suggest that mNGS be used as a crucial supplementary diagnostic tool for individuals with compromised immune systems who may have CSD, especially when conventional diagnostic methods are inconclusive.
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Affiliation(s)
- Tao Zhou
- Department of Infectious Disease Department, The Third People’s Hospital of Chengdu, Chengdu, China
| | - Yaqiu Zheng
- Digestive Endoscopy Center, Public Health Clinical Center of Chengdu, Chengdu, China
| | - Huizi Zhang
- Department of Geriatric, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Yongfang Liu
- Department of Infectious Disease Department, The Third People’s Hospital of Chengdu, Chengdu, China
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Pang F, Xu W, Zhao H, Chen S, Tian Y, Fu J, You Z, Song P, Xian Q, Zhao Q, Wang C, Jia X. Comprehensive evaluation of plasma microbial cell-free DNA sequencing for predicting bloodstream and local infections in clinical practice: a multicenter retrospective study. Front Cell Infect Microbiol 2024; 13:1256099. [PMID: 38362158 PMCID: PMC10868388 DOI: 10.3389/fcimb.2023.1256099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/12/2023] [Indexed: 02/17/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA (cfDNA) shows promising application for complicated infections that cannot be resolved by conventional microbiological tests (CMTs). The criteria for cfDNA sequencing are currently in need of agreement and standardization. Methods We performed a retrospective cohort observation of 653 patients who underwent plasma cfDNA mNGS, including 431 with suspected bloodstream infections (BSI) and 222 with other suspected systemic infections. Plasma mNGS and CMTs were performed simultaneously in clinical practice. The diagnostic efficacy of plasma mNGS and CMTs in the diagnosis of blood-borne and other systemic infections was evaluated using receiver operating characteristic (ROC) curves. The sensitivity and specificity of the two methods were analyzed based on the final clinical outcome as the gold standard. Results The mNGS test showed an overall positive rate of 72.3% (472/653) for detecting microorganisms in plasma cfDNA, with a range of 2 to 6 different microorganisms detected in 171 patient specimens. Patients with positive mNGS results were more immunocompromised and had a higher incidence of severe disease (P<0·05). The sensitivity of mNGS was higher for BSI (93·5%) and other systemic infections (83·6%) compared to CMTs (37·7% and 14·3%, respectively). The mNGS detected DNA from a total of 735 microorganisms, with the number of microbial DNA reads ranging from 3 to 57,969, and a higher number of reads being associated with clinical infections (P<0·05). Of the 472 patients with positive mNGS results, clinical management was positively affected in 203 (43%) cases. Negative mNGS results led to a modified clinical management regimen in 92 patients (14.1%). The study also developed a bacterial and fungal library for plasma mNGS and obtained comparisons of turnaround times and detailed processing procedures for rare pathogens. Conclusion Our study evaluates the clinical use and analytic approaches of mNGS in predicting bloodstream and local infections in clinical practice. Our results suggest that mNGS has higher positive predictive values (PPVs) for BSI and systemic infections compared to CMTs, and can positively affect clinical management in a significant number of patients. The standardized whole-process management procedure for plasma mNGS developed in this study will ensure improved pre-screening probabilities and yield clinically valuable data.
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Affiliation(s)
- Feng Pang
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Wenbin Xu
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Hui Zhao
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Shuai Chen
- Department of Clinical Laboratory, Liaocheng Thrid People’s Hospital, Liaocheng, Shandong, China
| | - Yaxian Tian
- Department of Center Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Juanjuan Fu
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Zhiqing You
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Pingping Song
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Qingjie Xian
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Qigang Zhao
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Chengtan Wang
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Xiuqin Jia
- The Key Laboratory of Molecular Pharmacology, Liaocheng People’s Hospital, Liaocheng, Shandong, China
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Shi Y, Peng JM, Hu XY, Yang QW, Wang Y. Metagenomic next-generation sequencing for detecting Aspergillosis pneumonia in immunocompromised patients: a retrospective study. Front Cell Infect Microbiol 2023; 13:1209724. [PMID: 38188627 PMCID: PMC10770824 DOI: 10.3389/fcimb.2023.1209724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Purpose The identification of Aspergillus by metagenomic next-generation sequencing (mNGS) remains a challenging task due to the difficulty of nucleic acid extraction. The objective of this study was to determine whether mNGS could provide an accurate and efficient method for detecting invasive pulmonary aspergillosis (IPA) in immunocompromised patients (ICP). Methods A total of 133 ICP admitted to the ICU between January 2020 and September 2022 were enrolled in the study, of which 46 were diagnosed with IPA and 87 were non-IPA cases. The bronchoalveolar lavage fluid (BALF) was analyzed for the presence of Aspergillosis and other co-pathogens using mNGS, and its diagnostic performance was compared to conventional microbial tests (CMTs) that included smear, cultures, serum and BALF galactomannan (GM) test. Clinical composite diagnosis was used as the reference standard. Results mNGS had a sensitivity, specificity, and accuracy of 82.6%, 97.7%, and 92.5%, respectively, in diagnosing IPA. These findings were comparable to those of the combination of multiple CMTs. Interestingly, the sensitivity of mNGS was superior to that of any single CMT method, as demonstrated by comparisons with smears (8.7%, P < 0.001), culture (39.1%, P < 0.001), serum GM (23.9%, P < 0.001) and BALF GM (69.6%, P = 0.031). mNGS was capable of accurately distinguish strains of Aspergillus genus, with a consistency of 77.8% with culture. Furthermore, mNGS also identified A. fumigatus, A. flavus, A. terrestris, A. oryzae and Mucor spp. in culture-negative cases. The sequencing reads of Aspergillus by mNGS exhibited extensive variation, ranging from 11 to1702. A positive correlation was observed between the optical density index of BALF GM and unique reads by mNGS (r = 0.607, P = 0.001) in BALF-GM positive patients. Notably, mNGS was able to diagnose 35 out of 37 cases with mixed infection, with P. jirovecii and cytomegalovirus being the most common co-pathogens. Conclusions mNGS presents a feasible and remarkably sensitive approach for detecting Aspergillus in ICP, thereby serving as a valuable adjunctive tool to CMT. Furthermore, mNGS's ability to accurately identify fungal species and co-pathogens can assist in guiding appropriate antimicrobial therapy.
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Affiliation(s)
- Yan Shi
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jin-Min Peng
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiao-Yun Hu
- Department of Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Qi-Wen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yao Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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Nie S, Zhang Q, Chen R, Lin L, Li Z, Sun Y, Huang J, Feng Z, Cao X, Ye K, Tang L, Zhou J, Cai G, Chen X. Rapid detection of pathogens of peritoneal dialysis-related peritonitis, especially in patients who have taken antibiotics, using metagenomic next-generation sequencing: a pilot study. Ren Fail 2023; 45:2284229. [PMID: 38031397 PMCID: PMC11001327 DOI: 10.1080/0886022x.2023.2284229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/10/2023] [Indexed: 12/01/2023] Open
Abstract
INTRODUCTION Peritoneal dialysis (PD)-related peritonitis is a serious complication of PD. Improving the diagnostic rate of peritonitis pathogens may substantially benefit peritonitis patients. METHODS The study was conducted in the People's Liberation Army (PLA) General Hospital from 1 June 2021 to 31 May 2022. Information about peritonitis, culture and metagenomic next-generation sequencing (mNGS) results and so on were collected. Patients were divided into antibiotic-use and antibiotic-free groups. The culture and mNGS results were compared using the paired χ2 test. RESULTS Data from 26 patients with peritonitis were collected. 50% of the patients had used antibiotics before samples were obtained (antibiotic-use group). The positivity rate using culture was 92.3% (12 cases) in the antibiotic-free group and 38.5% (5 cases) in the antibiotic-use group (p = 0.011). However, the positivity rate using mNGS was 92.3% (12 cases) regardless of whether antibiotics were used (p = 1.000). After revising the mNGS results, the positivity rate was 84.6% (11 cases) in both groups (p = 1.000). A significant difference between culture and mNGS results of all groups was observed (p = 0.039). The difference no matter between culture and mNGS (p = 0.016) or between culture and modified mNGS (p = 0.031) of the antibiotic-use group was observed. CONCLUSION For patients with PD-related peritonitis who previously received antibiotics, mNGS is suggested. For other patients, mNGS testing can be performed, but the results should be interpreted with caution. Much more research should be done to identify a powerful and ideal tool to detect pathogens underlying PD-related peritonitis.
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Affiliation(s)
- Sasa Nie
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Qingtao Zhang
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Rong Chen
- Department of clinical laboratory, the First Medical Center, Chinese PLA General Hospita, Beijing, China
| | - Li Lin
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Zhenzhen Li
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Yanli Sun
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Jing Huang
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Zhe Feng
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Xueying Cao
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Kun Ye
- Department of clinical laboratory, the First Medical Center, Chinese PLA General Hospita, Beijing, China
| | - Li Tang
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Jianhui Zhou
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Guangyan Cai
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
| | - Xiangmei Chen
- Department of Nephrology, the First Medical Center, Chinese PLA General Hospital, Nephrology Institute of the Chinese People’s Liberation Army, National Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing, China
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Xu L, Wu H, Zhou H, Zhou X, Sun Y. Purulent meningitis and secondary epilepsy caused by Mycobacterium iranicum infection: A case report. Int J Infect Dis 2023; 135:5-7. [PMID: 37327856 DOI: 10.1016/j.ijid.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023] Open
Abstract
Mycobacterium iranicum is characterized by rapid growth and orange-pigmented scotochromogenic colonies. However, it is uncommon for M. iranicum to invade the central nervous system. A man nearly 60 years old was referred to our hospital because of a seizure and unconsciousness. After admission, the patient had fever and dizziness without obvious abnormalities in the cerebrospinal fluid, except for an increase in neutrophils. Metagenomic next-generation sequencing and DNA testing were positive for M. iranicum. The patient was treated with imipenem, minocycline, moxifloxacin, and linezolid, and he gradually recovered during follow-up.
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Affiliation(s)
- Liaoyang Xu
- Department of Neurology, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China
| | - Huijuan Wu
- Department of Neurology, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China; Department of Neurology, Jinzhou Medical University, Jinzhou, China
| | - Hang Zhou
- Department of Hematology, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China
| | - Xinyu Zhou
- Department of Neurology, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China; Department of Neurology, The First Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang, China.
| | - Yong Sun
- Department of Neurology, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China; Department of Neurosurgery, The First Affiliated Hospital of Kangda College of Nanjing Medical University, Lianyungang, China.
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Pan X, Zhang Y, Chen G. The clinical utility of metagenomic next-generation sequencing for the diagnosis of central nervous system infectious diseases. Neurol Res 2023; 45:919-925. [PMID: 37615407 DOI: 10.1080/01616412.2023.2247299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/10/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND To evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) for the diagnosis of central nervous system infections (CNSI). METHODS Cerebrospinal fluid (CSF) from 54 patients who were high-level clinical suspicion of CNSI was collected and sent for mNGS and conventional tests from January 2019 to March 2022. RESULTS Twenty out of 54 patients were diagnosed with CNSI and 34 non-CNSI. Among the 34 non-CNSI, one was false positive by mNGS. Among the 20 CNSI, 11 had presumed viral encephalitis and/or meningitis, 5 had presumed bacterial meningitis, 2 had presumed TMB, 1 had Crytococcus meningitis and 1 had neurosyphilis. The sensitivity of viral encephalitis and/or meningitis was 0.73 (8/11); 10 virus were detected; 9/10 was dsDNA; 1/10 was ssRNA. SSRN ranged from 1 to 13. The accuracy rate was 0.4, the accuracy rate was positively correlated with SSRN (r = 0.738, P = 0.015), SSRN ≥ 1, the accuracy rate was 0.4; SSRN ≥ 3, the accuracy rate was 0.66; SSRN ≥ 4, the accuracy rate was 0.75; SSRN ≥ 6, the accuracy rate was 1. The sensitivity of bacterial meningitis was 1. Seven kinds of bacteria were detected, among which 3/7 were gram positive, 3/7 were gram negative, and 1/7 was infected NTM (nontuberculous mycobacteria). The accuracy rate was 0.43 (3/7). The sensitivity of TBM was 0.66 (2/3), the accuracy rate was 1. The sensitivity of Crytococcus meningitis was 1, the accuracy rate was 0.5. PPV (positive predictive value) of mNGS was 0.94, NPV (negative predictive value) of mNGS was 0.89, specificity was 0.97 and sensitivity was 0.8. The AUG for CSF mNGS diagnosis of CNSI was 0.89 (95% CI = 0.78-0.99) Headache, meningeal irritation sign and image of meninges abnormal were correlated with the sensitivity of mNGS (r = 0.451, 0.313, 0.446; p = 0.001, 0.021, 0.001); CSF Glucose and CSF Chloride were negatively correlated with sensitivity of mNGS (r = -0.395, -0.462; p = 0.003, < 0.001). CONCLUSION mNGS is a detection means with high sensitivity, wide coverage and strong timeliness, which can help clinicians to identify the pathogen diagnosis quickly, conduct targeted anti-infection treatment early and reduce antibiotic abuse. The pathogen which causing low CSF Glucose, low CSF Chloride or meninges infections was more likely to be detected by mNGS. It may be related to growth and structural characteristics of the pathogen and blood-brain barrier damage.
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Affiliation(s)
- Xiaoying Pan
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuefeng Zhang
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guohua Chen
- Department of Neurology, The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
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Yang L, Peng L, Yuan K, Cai K, Feng C, Yang G, Wang S, Zhu X, Zhang J, Wang F, Lu H. Case Report: Mycobacterium kansasii causing infective endocarditis explored by metagenomic next-generation sequencing. Front Cell Infect Microbiol 2023; 13:1227537. [PMID: 37680745 PMCID: PMC10482420 DOI: 10.3389/fcimb.2023.1227537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/01/2023] [Indexed: 09/09/2023] Open
Abstract
In this report, we describe the first case of infective endocarditis caused by Mycobacterium kansasii in a 45-year-old male patient who presented with a 10-day fever and decompensated cirrhosis. Despite negative results in blood culture and pathology, we employed metagenomic next-generation sequencing (mNGS) to analyze the genome sequences of both the host and microbe. The copy number variation (CNV) indicated a high risk of liver disease in the patient, which correlated with biochemical examination findings. Notably, M. kansasii sequences were detected in peripheral blood samples and confirmed through Sanger sequencing. Unfortunately, the patient's condition deteriorated, leading to his demise prior to heart surgery. Nevertheless, we propose that mNGS could be a novel approach for diagnosing M. kansasii infection, particularly in cases where blood culture and pathology results are unavailable. It is important to consider M. kansasii infection as a potential cause of endocarditis and initiate appropriate anti-infection treatment.
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Affiliation(s)
- Liuqing Yang
- The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Ling Peng
- The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Ke Yuan
- BGI Genomics, BGI Shenzhen, Shenzhen, China
| | - Kanru Cai
- The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Cheng Feng
- The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Gendong Yang
- The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | | | - Xiuyun Zhu
- The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Jieyun Zhang
- The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Fuxiang Wang
- The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Hongzhou Lu
- The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
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Zhou Q, Zhan Z, Huang F, Zhao M, Huang D, Xu J, Huang L, Xie L, Zhang A. Case report: A rare multidrug-resistant Escherichia coli causes fatal neonatal meningoencephalitis. Front Public Health 2023; 11:1174536. [PMID: 37575122 PMCID: PMC10420072 DOI: 10.3389/fpubh.2023.1174536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Neonatal meningitis is rare but devastating disease. Multidrug-resistant (MDR, multi-drug resistant) bacteria are a major global health risk. We report an Escherichia coli meningitis isolate with multiple resistance patterns and unusual serotype (O75) that caused sudden neonatal death. The isolate was resistant to antibiotics other than cefoperazone/sulbactam and imipenem, challenging the combination of antibiotics commonly used in the empirical treatment of neonatal sepsis. Despite aggressive symptomatic and supportive treatment of the infant based on laboratory tests and clinical practice, the infant eventually died. This is the first case of meningoencephalitis due to serotype O75 reported in China. The presence of highly pathogenic multidrug-resistant microorganisms isolated in neonates underscores the need to implement rapid resistance diagnostic methods and should prompt consideration of alternatives to empiric treatment of neonatal bacterial meningitis.
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Affiliation(s)
- Qingyun Zhou
- The First-Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, Hunan, China
| | - Zhifei Zhan
- Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Furong Huang
- The First-Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, Hunan, China
| | - Menghua Zhao
- The First-Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, Hunan, China
| | - Daosheng Huang
- The First-Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, Hunan, China
| | - Jun Xu
- The First-Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, Hunan, China
| | - Li Huang
- The First-Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, Hunan, China
| | - Liangyi Xie
- The First-Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, Hunan, China
| | - Aimin Zhang
- The First-Affiliated Hospital of Hunan Normal University, Hunan Provincial People's Hospital, Changsha, Hunan, China
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Wang C, Wang J, Yan J, Chen F, Zhang Y, Hu X. Mycoplasma hominis, Ureaplasma parvum and Ureaplasma urealyticum: hidden pathogens in peritoneal dialysis-associated peritonitis. Int J Infect Dis 2023; 131:13-15. [PMID: 36948449 DOI: 10.1016/j.ijid.2023.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/21/2023] [Accepted: 03/12/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Mycoplasma hominis, Ureaplasma parvum, and Ureaplasma urealyticum commonly colonize the human urogenital tract which may cause urogenital infections. However, infection by M. hominis, U. parvum, or U. urealyticum is rarely reported in peritoneal dialysis (PD) associated peritonitis patients. Herein, we reported four cases of PD-associated peritonitis caused by these pathogens, along with a review of the literature. CASE REPORT The four cases were female patients with recurrent "culture-negative" PD-associated peritonitis and were related to menstruation. M. hominis, U. parvum, or U. urealyticum was detected in the peritoneal dialysis fluid of the patients by metagenomic next-generation sequencing (mNGS). All four patients were cured by intraperitoneal (IP) tigecycline combined with oral azithromycin or minocycline. CONCLUSIONS M. hominis, U. parvum, and U. urealyticum should be paid more attention in female patients suffering from recurrent "culture-negative" PD-associated peritonitis, especially when the peritonitis is related to menstruation, sexual intercourse, or urogenital tract operation. Moreover, mNGS can provide a reasonable method to identify the pathogen for "culture-negative" PD-associated peritonitis.
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Affiliation(s)
- Can Wang
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Jingshuang Wang
- Department of Nephrology, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Juan Yan
- Department of Nephrology, The people's hospital of liangping, Chongqing, China; Department of Nephrology, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Feng Chen
- Department of Nephrology, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Ying Zhang
- Department of Nephrology, The Second Affiliated Hospital of Army Medical University, Chongqing, China.
| | - Xuelian Hu
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China.
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Zhu N, Zhou D, Yuan R, Ruzetuoheti Y, Li J, Zhang X, Li S. Identification and comparison of Chlamydia psittaci, Legionella and Mycoplasma pneumonia infection. Clin Respir J 2023; 17:384-393. [PMID: 36929690 DOI: 10.1111/crj.13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
INTRODUCTION Conventional etiological detection and pathogenic antibody methods make it challenging to identify the atypical pathogens among the community-acquired pneumonia (CAP). Metagenomic next-generation sequencing (mNGS) could rapidly detect all potentially infectious diseases and identifies novel or potential pathogens. METHODS Eighteen patients diagnosed with atypical CAP were enrolled in this retrospective study, including nine Chlamydia psittaci pneumonia (C. p), four Legionella pneumonia (L. p) and five Mycoplasma pneumonia (M. p). We simultaneously tested bronchoalveolar lavage fluid (BALF) samples for conventional microbiological methods and mNGS, and blood specimens were analysed. We also collected and compared baseline and clinical characteristics and treatment responses. RESULTS Patients with C. p and L. p had similar symptoms, including fever, cough, headache, dyspnoea, asthenia, shivering and headache, compared with M. p, whose symptoms were slight. C. p and L. p usually showed multiple lobar distributions with pleural effusion. Serologic testing indicated that L. p had higher levels of white blood cells (WBCs), neutrophils, C-reactive protein (CRP), procalcitonin (PCT), alanine aminotransferase (ALT), lactate dehydrogenase (LDH) and creatinine compared with M. p and L. p (p < 0.05). However, patients with C. p had lower levels of albumin (p < 0.05), and M. p had a minimum risk of cardiac volume loads (p < 0.05). CD4/CD8 ratio, lymphocytes, aspartate aminotransferase (AST), creatine kinase (CK), cell counting of BALF and coagulation had no difference (p < 0.05). Pathogenic IgM assay showed that 4/5 cases were positive for M. p and no positive detection for C. p and L. p infection. We timely adjusted the antibiotics according to the final mNGS results. Eventually, 16/18 patients recovered fully. Conditions of L. p patients were worse than those of C. p patients, and those of M. p patients were the least. CONCLUSION Early application of mNGS detection increased the atypical pathogenic identification, improved the prognosis and made up for the deficiency of conventional detection methods.
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Affiliation(s)
- Ning Zhu
- Department of Respiratory and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Daibing Zhou
- Department of Respiratory and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Ruyu Yuan
- Department of Respiratory and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yiminniyaze Ruzetuoheti
- Department of Respiratory and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Li
- Department of Respiratory and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiujuan Zhang
- Department of Respiratory and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Shengqing Li
- Department of Respiratory and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
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Huang Y, Zheng W, Gan W, Zhang T. Chlamydia psittaci pneumonia: a clinical analysis of 12 patients. Ann Transl Med 2023; 11:144. [PMID: 36846017 PMCID: PMC9951019 DOI: 10.21037/atm-22-6624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/29/2023] [Indexed: 02/08/2023]
Abstract
Background We conducted a retrospective analysis to explore the clinical characteristics, laboratory examination, imaging features, treatment outcomes, and prognosis of the Chlamydia psittaci (C. psittaci) pneumonia, aiming to improve early diagnosis and treatment. Methods The clinical data of 12 patients with C. psittaci pneumonia diagnosed by metagenomic next-generation sequencing (mNGS) in our hospital were retrospectively analyzed. These data included baseline information, epidemiological history, clinical symptoms and signs, laboratory and chest computed tomography (CT) examination findings, treatment schemes, and prognosis. Results The average age of the 12 patients was 58.25±13.27 years, and there were 7 (58.3%) males and 5 (41.7%) females in this cohort. Five patients had clear exposure to poultry or birds. The main clinical manifestations included fever (12/12, 100.0%), cough (12/12, 100.0%), expectoration (10/12, 83.3%), and dyspnea (10/12, 83.3%). Laboratory examination showed marked elevation of the total white blood cell (WBC) count, neutrophil (NEUT) count, C-reactive protein (CRP), procalcitonin (PCT), D-dimer, aspartate aminotransferase (AST), alanine aminotransferase (ALT), serum creatinine, and creatine kinase (CK) levels; as well as decreased hemoglobin (HGB), blood platelet (PLT), and albumin (ALB) levels. Arterial blood gas analysis showed that the average value of the oxygenation index (PO2/FiO2) was 290.9±83.1, which was less than 300 in 6 cases (50.0%). The main chest CT features were patchy or consolidation in the bilateral or unilateral lungs, and the boundary was not clear but showed a bronchial inflation sign. Also, some of the cases were accompanied by pleural effusion. Once the etiology was obtained, the patients were quickly treated with doxycycline combined with other antibiotics. All 12 patients improved and were discharged from the hospital. However, two severe patients were admitted to the intensive care unit (ICU) and received ventilation and monitoring treatment. There were no deaths. Conclusions C. psittaci pneumonia is an atypical community-acquired pneumonia (CAP) caused by C. psittaci infection, with its own laboratory and imaging characteristics. In this study, diagnosis was established based on the application of mNGS owing to the absence of easily available conventional pathogenic evidence. In addition, an aggressive and precise treatment strategy can help achieve a favorable prognosis for patients.
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Affiliation(s)
- Yubo Huang
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenzheng Zheng
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenlei Gan
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Tiantuo Zhang
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Lin P, Chen Y, Xu J, Huang X, Wen W, Zhang L, Kong W, Zhao Z, Ye Y, Bao Z, Song Y, Lin S, Yu Z. A multicenter-retrospective cohort study of chromosome instability in lung cancer: clinical characteristics and prognosis of patients harboring chromosomal instability detected by metagenomic next-generation sequencing. J Thorac Dis 2023; 15:112-122. [PMID: 36794146 PMCID: PMC9922610 DOI: 10.21037/jtd-22-1732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023]
Abstract
Background The usefulness of metagenomic next-generation sequencing (mNGS) in identifying the prognosis of lung cancer with chromosomal instability (CIN) remains unclear. We aimed to analyze clinical characteristics and prognosis of patients in patients harboring CIN. Methods This retrospective cohort study included 668 patients diagnosed with suspected pulmonary infection or lung cancer whose samples underwent mNGS detection from January 2021 to January 2022. Difference between clinical characteristics were calculated by the Student's t-test and the chi-square test. The subjects were followed-up from registered to September 2022. Survival curves were analyzed by the Kaplan-Meier method. Results Of 619 bronchoalveolar lavage fluid (BALF) samples collected by bronchoscopy, 30 CIN-positive samples were confirmed as malignant on histopathology, with a sensitivity of 61.22%, a specificity of 99.65%, and an 83.17% accuracy [cut-off values were established by the receiver operating characteristic (ROC) area under the curve (AUC) =0.804]. In 42 patients with lung cancer, mNGS detected 24 patients as CIN-positive and 18 as CIN-negative. There were no differences between two groups including ages, pathologic types, stage and metastases. In 25 cases, we detected 523 chromosomal copy number variants (CNVs) with forms including duplication (dup), deletion (del), mosaic (mos), and whole chromosome amplification or loss. A total of 243 duplication variants and 192 deletion variants occurred in all chromosomes. Duplications occurred in most chromosomes except for Chr9 and Chr13, in which CNV tended to delete. The median overall survival (OS) in patients with Chr5p15 duplication was 32.4 months [95% confidence interval (CI), 10.35-54.45 months]. The median OS differed significantly between the 5p15dup+ group and the combined group (32.4 vs. 8.63 months, P=0.049). In 29 patients with unresected lung cancer, the median OS of 18 cases in the CIN-positive group was 32.4 months (95% CI, 14.2-50.6 months) and the median OS of 11 cases in the CIN-negative group was 35.63 months (95% CI, 21.64-49.62 months; Wilcoxon, P=0.227). Conclusions Various forms of CIN detected by mNGS may predict prognosis of patients with lung cancer differentially. CIN with duplication or deletion deserves further study to guide clinical treatment.
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Affiliation(s)
- Ping Lin
- Fuzong Clinical Medicine, Fujian Medical University, Fuzhou, China
| | - Ying Chen
- Fuzong Clinical Medicine, Fujian Medical University, Fuzhou, China
| | - Jinhe Xu
- Department of Pulmonary and Critical Care Medicine, The 900th Hospital of the Joint Logistic Support Force, Fujian Medical University, Fuzhou, China
| | - Xiulian Huang
- Department of Pulmonary and Critical Care Medicine, The 900th Hospital of the Joint Logistic Support Force, Fujian Medical University, Fuzhou, China
| | - Wen Wen
- Department of Pulmonary and Critical Care Medicine, The 900th Hospital of the Joint Logistic Support Force, Fujian Medical University, Fuzhou, China
| | - Lei Zhang
- Department of Pulmonary and Critical Care Medicine, The 900th Hospital of the Joint Logistic Support Force, Fujian Medical University, Fuzhou, China
| | - Wencui Kong
- Department of Pulmonary and Critical Care Medicine, The 900th Hospital of the Joint Logistic Support Force, Fujian Medical University, Fuzhou, China
| | - Zhongquan Zhao
- Department of Pulmonary and Critical Care Medicine, The 900th Hospital of the Joint Logistic Support Force, Fujian Medical University, Fuzhou, China
| | - Ya Ye
- Department of Pulmonary and Critical Care Medicine, The 900th Hospital of the Joint Logistic Support Force, Fujian Medical University, Fuzhou, China
| | - Zhenming Bao
- Department of Pulmonary and Critical Care Medicine, The 900th Hospital of the Joint Logistic Support Force, Fujian Medical University, Fuzhou, China
| | - Yingfang Song
- Department of Pulmonary and Critical Care Medicine, The 900th Hospital of the Joint Logistic Support Force, Fujian Medical University, Fuzhou, China
| | - Shaoqing Lin
- Department of Pulmonary and Critical Care Medicine, The 900th Hospital of the Joint Logistic Support Force, Fujian Medical University, Fuzhou, China
| | - Zongyang Yu
- Department of Pulmonary and Critical Care Medicine, The 900th Hospital of the Joint Logistic Support Force, Fujian Medical University, Fuzhou, China
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Zhang B, Chen X, Yao X, Li M, Li Z, Liu B, Liu S, Liu Z, Huo J, Han Y. The diagnostic value of blood metagenomic next-generation sequencing in patients with acute hematogenous osteomyelitis. Front Cell Infect Microbiol 2023; 13:1106097. [PMID: 36779189 PMCID: PMC9911542 DOI: 10.3389/fcimb.2023.1106097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/16/2023] [Indexed: 01/28/2023] Open
Abstract
Aims This study aims to evaluate the diagnostic value of blood metagenomic next-generation sequencing (mNGS) in detecting pathogens from patients clinically diagnosed as acute hematogenous osteomyelitis (AHO). Methods This retrospective study enrolled 66 patients with AHO. The test results of mNGS and bacterial culture on different samples, including blood and puncture fluid samples, from patients with AHO were compared to explore the diagnostic value of blood mNGS. Besides, this study also explored the efficacy of blood mNGS in decision making for antibiotic administration and analyzed the factors associated with the positive result of blood mNGS. Results The most common causative pathogens were Staphylococcus and Streptococcus. The sensitivity of blood mNGS (77.3%) was higher than that of blood culture (42.4%) (P<0.001), while the turnaround time of blood mNGS (2.1 ± 0.4 d) is much less than that of blood culture (6.0 ± 2.1 d) (P<0.001). Besides, the sensitivity of blood mNGS tests (77.3%) was slightly lower than that of puncture fluid mNGS (89.4%). Furthermore, detection comparison at pathogen level unravels that blood mNGS might be suitable for diagnosing AHO caused by common pathogens, while puncture fluid mNGS could be considered as preferred examination in diagnosing AHO caused by uncommon pathogens. Finally, three independent factors associated with the true positive result of blood mNGS in patients with AHO were identified, including Gram-positive pathogens (OR=24.4, 95% CI = 1.4-421.0 for Staphylococcus; OR=14.9, 95%CI= 1.6-136.1 for other Gram-positive bacteria), body temperature at sampling time (OR=8.2, 95% CI = 0.6-107.3 for body temperature of >38.5°C; OR=17.2, 95% CI = 2.0-149.1 for patients who were chilling), and no use of antibiotics before sampling (OR=8.9, 95% CI =1.4-59.0). Conclusion This is the first report on evaluating and emphasizing the importance of blood mNGS in diagnosing AHO. Blood sample might be an alternative sample for puncture fluid for mNGS, and its extensive application in diagnosing AHO could be expected.
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Affiliation(s)
- Bingshi Zhang
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Xiao Chen
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Xiaowei Yao
- Department of Orthopedics, The Chest Hospital of Hebei Province, Shijizhuang, Hebei, China
| | - Mengnan Li
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Zhijie Li
- Orthopedics Department, Affiliated Hospital of Hebei Engineering University, Handan, Hebei, China
| | - Bo Liu
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Sikai Liu
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Zeming Liu
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Jia Huo
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China
| | - Yongtai Han
- Department of Osteonecrosis and Hip Surgery, The Third Hospital of Hebei Medical, Shijiazhuang, Hebei, China,*Correspondence: Yongtai Han,
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Wang J, Xu H, Wang X, Lan J. Rapid diagnosis of non-tuberculous mycobacterial pulmonary diseases by metagenomic next-generation sequencing in non-referral hospitals. Front Cell Infect Microbiol 2023; 12:1083497. [PMID: 36760234 PMCID: PMC9902348 DOI: 10.3389/fcimb.2022.1083497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/21/2022] [Indexed: 01/26/2023] Open
Abstract
Objectives The incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has increased steadily globally, but the current culture-based diagnosis of NTM-PD is difficult and time-consuming, leading to a high possibility of misdiagnosis. Therefore, new methods should be introduced to improve the processes for clinical diagnosis of this disease. Methods Our retrospective observational study enrolled 12 NTM-PD patients who were identified by way of metagenomic next-generation sequencing (mNGS), as well as the characteristic radiological presentation of slowly progressed, usually concomitant bronchiectasis, small cavitary opacity, and multiple nodules that respond poorly to empirical antibiotic therapy. These patients received the recommended drug regimen based on the identified non-tuberculous mycobacteria (NTM) species. Clinical data, including symptoms, laboratory tests, dynamic computed tomography imaging, treatment, and outcome, were recorded and analyzed. Results The results of mNGS were all positive, with the standard specifically mapped read numbers (SDSMRN) of NTM ranging from 1 to 766; this was confirmed in six patients via quantitative polymerase chain reaction (qPCR) analysis. The duration fromsample collection tomNGS results was 1-4 days. Among our 12 patients (except for one lost to follow-up) the CT imaging for 11 patients showed significant absorption of lesions. Conclusions Our results draw attention to NTM infection as a possible cause of community-acquired pneumonia, especially in patients with suggestive radiological presentation and poor responses to empirical antibiotic therapy. Our study also indicated that mNGS represented a potentially effective tool for the rapid identification of NTM in the respiratory sample. Improved clinician awareness combined with the utilization of mNGS could guide earlier diagnosis and targeted treatment, and finally improved the prognoses of patients with NTM-PD.
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Affiliation(s)
- Jing Wang
- Department of Respiratory and Critical Care Medicine, the Second Clinical Hospital of Chongqing Medical University, Chongqing, China
| | - Huan Xu
- Department of Scientific Affairs, Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Xi Wang
- Department of Respiratory and Critical Care Medicine, the Second Clinical Hospital of Chongqing Medical University, Chongqing, China
| | - Jian Lan
- Department of Respiratory and Critical Care Medicine, the Second Clinical Hospital of Chongqing Medical University, Chongqing, China,*Correspondence: Jian Lan,
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Zhuang H, Xiang K, Gong S, Zhou Y, Chen J. Cerebral aspergillosis after heart-lung transplantation in a child: Case report with 3-year follow-up and literature review. Front Cardiovasc Med 2023; 9:1042631. [PMID: 36684597 PMCID: PMC9853382 DOI: 10.3389/fcvm.2022.1042631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/13/2022] [Indexed: 01/08/2023] Open
Abstract
There are limited cases of heart-lung transplantation (HLT) in children worldwide owing to lack of donors, demanding surgical teamwork, and arduous post-operative management. Post-transplant management difficulties stem from the possible development of several post-operative complications, with infection being a common complication. Intracranial fungal infections are difficult to diagnose and prone to treatment delays because of their relatively insidious onset and atypical clinical presentation. Here, we present a case of a cerebral infection developed 3 months after HLT in a 10-year-old child, showing no positive results on conventional imaging or cerebrospinal fluid (CSF) examination and culture. On metagenomic next-generation sequencing of the cerebrospinal fluid, the causative organism was finally determined as Aspergillus. After administering 1-year anti-Aspergillus treatment, no recurrence of intracranial fungal infection was noted during the 3-year follow-up. This case illustrates the multifaceted diagnostic techniques for cerebral aspergillosis after HLT and shows the significance of dynamic monitoring of symptoms, such as headache, and of metagenomic sequencing results, trends in intracranial pressure and (1-3)-β-D-glucan levels for guiding diagnosis and treatment.
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Affiliation(s)
- Huanwei Zhuang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China,Department of Cardiac Surgery, Haikou Affiliated Hospital of Central South University Xiangya School of Medicine, Haikou, China
| | - Kun Xiang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Shuji Gong
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yangang Zhou
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jinlan Chen
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Jinlan Chen,
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Jia K, Huang S, Shen C, Li H, Zhang Z, Wang L, Zhao G, Wu Z, Lin Y, Xia H, Tang M, Yang H, Hu H. Enhancing urinary tract infection diagnosis for negative culture patients with metagenomic next-generation sequencing (mNGS). Front Cell Infect Microbiol 2023; 13:1119020. [PMID: 36936777 PMCID: PMC10020507 DOI: 10.3389/fcimb.2023.1119020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a promising technology that allows unbiased pathogen detection and is increasingly being used for clinical diagnoses. However, its application in urinary tract infection (UTI) is still scarce. Methods The medical records of 33 patients with suspected UTI who were admitted to the Second Hospital of Tianjin Medical University from March 2021 to July 2022 and received urine mNGS were retrospectively analyzed. The performance of mNGS and conventional urine culture in diagnosing infection and identifying causative organisms was compared, and the treatment effects were evaluated in terms of changes in urinalyses and urinary symptoms. Results In the detection of bacteria and fungi, mNGS detected at least one pathogen in 29 (87.9%) cases, including 19 (57.6%) with positive mNGS but negative culture results and 10 (30.3%) with both mNGS and culture positive results. The remaining 4 (12.1%) patients were negative by both tests. Overall, mNGS performed better than culture (87.9% vs. 30.3%, P < 0.001). Within the 10 double-positive patients, mNGS matched culture results exactly in 5 cases, partially in 4 cases, and not at all in 1 case. In addition, mNGS detected a broader pathogen spectrum, detecting 26 species compared to only 5 species found in culture. The most abundant bacteria detected by mNGS was Escherichia coli, detected in 9 (27.2%) patients. All anaerobic bacteria, Mycobacterium Tuberculosis and all mixed pathogens were detected by mNGS. The final clinical diagnosis of UTI was made in 25 cases, and the sensitivity of mNGS was significantly higher than culture (100.0% vs 40.0%; P < 0.001) when using the diagnosis as a reference standard; the positive predictive value, negative predictive value and specificity were 86.2%, 100% and 50.0%, respectively. Importantly, targeted antibiotic therapy based on mNGS resulted in significant improvement in urinalyses and urinary symptoms in patients. Conclusions mNGS is a technology that has shown clear advantages over culture, particularly in the context of mixed infections and UTIs that are difficult to diagnose and treat. It helps to improve the detection of pathogens, guide changes in treatment strategies, and is an effective complement to urine culture.
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Affiliation(s)
- Kaipeng Jia
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Shiwang Huang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Chong Shen
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Hongjun Li
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhe Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Lei Wang
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Gangjian Zhao
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhouliang Wu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yuda Lin
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Mingze Tang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Huifen Yang
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
- *Correspondence: Huifen Yang, ; Hailong Hu,
| | - Hailong Hu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- *Correspondence: Huifen Yang, ; Hailong Hu,
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Liu G, Wang L, Li X, Zhang Y, Long H, Wang Y, Gao H, Xia H, Qian S. The value of next-generation metagenomic sequencing in pathogen detection of pleural effusions and ascites from children with sepsis. Front Cell Infect Microbiol 2023; 13:1130483. [PMID: 36891155 PMCID: PMC9986937 DOI: 10.3389/fcimb.2023.1130483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Objective To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) using pleural effusion and ascites from children with sepsis. Methods In this study, children with sepsis or severe sepsis and appeared pleural or peritoneal effusions were enrolled, of whom the pleural effusions or ascites and blood samples were conducted pathogen detection using both conventional and mNGS methods. The samples were divided into pathogen-consistent and pathogen-inconsistent groups based on the consistency of mNGS results from different sample types, and into exudate and transudate groups based on their pleural effusion and ascites properties. The pathogen positive rates, pathogen spectrum, consistency between different sample types, and clinical diagnosis consistency were compared between mNGS and conventional pathogen tests. Results A total of 42 pleural effusions or ascites and 50 other type samples were collected from 32 children. The pathogen positive rate of the mNGS test was significantly higher than that of traditional methods (78.57% vs. 14.29%, P < 0.001) in pleural effusion and ascites samples, with a consistent rate of 66.67% between the two methods. Nearly 78.79% (26/33) of mNGS positive results of the pleural effusions and ascites samples were consistent with clinical evaluation, and 81.82% (27/33) of these positive samples reported 1-3 pathogens. The pathogen-consistent group outperformed the pathogen-inconsistent group in terms of consistency with respect to clinical evaluation (88.46% vs. 57.14%, P = 0.093), while there was no significant difference between the exudate and transudate groups (66.67% vs. 50.00%, P = 0.483). Conclusion Compared to conventional methods, mNGS has great advantages in pathogen detection of pleural effusion and ascites samples. Moreover, consistent results of mNGS tests with different sample types provide more reference values in clinical diagnosis.
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Affiliation(s)
- Gang Liu
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Lijuan Wang
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Xuming Li
- Department of scientific affairs, HugoBiotech Co., Ltd., Beijing, China
| | - Ye Zhang
- Department of scientific affairs, HugoBiotech Co., Ltd., Beijing, China
| | - Hu Long
- Department of scientific affairs, HugoBiotech Co., Ltd., Beijing, China
| | - Yi Wang
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Hengmiao Gao
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Han Xia
- Department of scientific affairs, HugoBiotech Co., Ltd., Beijing, China
- *Correspondence: Suyun Qian, ; Han Xia,
| | - Suyun Qian
- Department of Pediatric Intensive Care Unit, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- *Correspondence: Suyun Qian, ; Han Xia,
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21
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Wang YL, Guo XT, Zhu MY, Mao YC, Xu XB, Hua Y, Xu L, Jiang LH, Zhao CY, Zhang X, Sheng GX, Jiang PF, Yuan ZF, Gao F. Metagenomic next-generation sequencing and proteomics analysis in pediatric viral encephalitis and meningitis. Front Cell Infect Microbiol 2023; 13:1104858. [PMID: 37153144 PMCID: PMC10161730 DOI: 10.3389/fcimb.2023.1104858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/22/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction Early and accurate identification of pathogens is essential for improved outcomes in patients with viral encephalitis (VE) and/or viral meningitis (VM). Methods In our research, Metagenomic next-generation sequencing (mNGS) which can identify viral pathogens unbiasedly was performed on RNA and DNA to identify potential pathogens in cerebrospinal fluid (CSF) samples from 50 pediatric patients with suspected VEs and/or VMs. Then we performed proteomics analysis on the 14 HEV-positive CSF samples and another 12 CSF samples from health controls (HCs). A supervised partial least squaresdiscriminant analysis (PLS-DA) and orthogonal PLS-DA (O-PLS-DA) model was performed using proteomics data. Results Ten viruses in 48% patients were identified and the most common pathogen was human enterovirus (HEV) Echo18. 11 proteins overlapping between the top 20 DEPs in terms of P value and FC and the top 20 proteins in PLS-DA VIP lists were acquired. Discussion Our result showed mNGS has certain advantages on pathogens identification in VE and VM and our research established a foundation to identify diagnosis biomarker candidates of HEV-positive meningitis based on MS-based proteomics analysis, which could also contribute toward investigating the HEV-specific host response patterns.
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Affiliation(s)
- Yi-Long Wang
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Xiao-Tong Guo
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Meng-Ying Zhu
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Yu-Chen Mao
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Xue-Bin Xu
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Yi Hua
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Lu Xu
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Li-Hua Jiang
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Cong-Ying Zhao
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Xin Zhang
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Guo-Xia Sheng
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Pei-Fang Jiang
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Zhe-Feng Yuan
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
| | - Feng Gao
- Department of Neurology, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, Zhejiang, China
- *Correspondence: Feng Gao,
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Li S, Qin J, Zhou P, Peng M, Qian J, Cai Y, Shi Q, Tung TH, Shen B, Yu S. The clinical significance of in-house metagenomic next-generation sequencing for bronchoalveolar lavage fluid diagnostics in patients with lower respiratory tract infections. Front Cell Infect Microbiol 2022; 12:961746. [PMID: 36590589 PMCID: PMC9801411 DOI: 10.3389/fcimb.2022.961746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
Objective Metagenomic next-generation sequencing (mNGS) technology has the potential to detect a wide range of pathogenic microorganisms. However, reports on the diagnostic value and clinical significance of different platforms of mNGS for patients with lower respiratory tract infections (LRTIs) remain scarce. Methods A total of 306 patients with suspected LRTIs were enrolled from January 2019 to December 2021. The diagnostic performance of conventional methods and mNGS on bronchoalveolar lavage fluid (BALF) were compared. BALF mNGS was performed using a commercial and an in-house laboratory. The diagnostic value and the clinical implications of mNGS for LRTIs were analyzed for the different platforms. Results The positive rate of mNGS in the in-house group was higher than that in the commercial group (85.26% vs. 70.67%, p < 0.001). mNGS significantly increased the pathogen detection rate compared with conventional methods [from 70.67% vs. 22.67% (p < 0.001) to 85.26% vs. 30.77% (p < 0.001)]. The pathogens detected using mNGS included bacteria, fungi, viruses, and atypical pathogens. The in-house platform performed well on a wider spectrum of microbial distribution. Furthermore, it showed an advantage in detecting mixed pathogens in immunocompromised patients. Among the mNGS positive cases, 34 (32.0%) cases had their antibiotics adjusted in the commercial group, while 51 (38.3%) cases had a change of treatment in the in-house group. Moreover, the turnaround time of mNGS and the time from mNGS to discharge in the in-house group were significantly shorter than those in the commercial group. Conclusion In-house mNGS had a higher detection rate and can show a wider spectrum of pathogens, with potential benefits for the clinic by shortening the turnaround time and hospitalization, and it may be more suitable for clinical microbiology laboratories.
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Affiliation(s)
- Shixiao Li
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Jiajia Qin
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Peng Zhou
- Department of Pharmacy, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Minfei Peng
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Jiao Qian
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Yingying Cai
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Qingxin Shi
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Tao-Hsin Tung
- Evidence-Based Medicine Center, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Bo Shen
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Sufei Yu
- Department of Clinical Microbiology Laboratory, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China,*Correspondence: Sufei Yu,
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Zhou X, Peng S, Song T, Tie D, Tao X, Jiang L, Zhang J. Neurosyphilis with ocular involvement and normal magnetic resonance imaging results affirmed by metagenomic next-generation sequencing. Front Cell Infect Microbiol 2022; 12:985373. [PMID: 36530424 PMCID: PMC9756949 DOI: 10.3389/fcimb.2022.985373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/10/2022] [Indexed: 12/04/2022] Open
Abstract
The rapid and accurate identification of pathogenic agents is the key to guide clinicians on diagnosis and medication, especially for intractable diseases, such as neurosyphilis. It is extremely challenging for clinicians to diagnose neurosyphilis with no highly sensitive and specific test available. It is well known that the early transmission and immune evasion ability of Treponema pallidum have earned it the title of "stealth pathogen." Neurosyphilis has complex clinical manifestations, including ocular involvement, which is infrequent and often overlooked, but its neuroimaging results may be normal. Therefore, it is important to find a new test that can detect the presence or absence of Treponema pallidum immediately for the diagnosis of neurosyphilis. We reviewed all the patients admitted to the Sichuan Provincial People's Hospital between 2021 and 2022 who had ocular involvement and whose clinical samples were examined via metagenomic next-generation sequencing (mNGS), and we found 10 candidates for further analysis. The results of magnetic resonance imaging (MRI) were normal for four patients, and three of them met the diagnostic criteria for neurosyphilis confirmed by mNGS. In addition, the results of mNGS from the three patients were further validated using polymerase chain reaction (PCR). Five of the 10 patients had diplopia manifestations; two (20%) experienced abducens nerve palsies, two (20%) had eyelid drooping, and one (10%) had decreased vision. One of the 10 patients (10%) who was HIV positive and five patients had abnormal MRI results. To our knowledge, Treponema pallidum was detected by mNGS in patients with ocular involvement and normal MRI results for the first time. Given this situation, we recommend mNGS as a potential and supplementary tool for the diagnosis and differential diagnosis of neurosyphilis.
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Affiliation(s)
- Xiaoli Zhou
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China,Sichuan Translational Medicine Research Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Shengkun Peng
- Sichuan Translational Medicine Research Hospital, Chinese Academy of Sciences, Chengdu, China,Department of Radiology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Tiange Song
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China,Sichuan Translational Medicine Research Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Dandan Tie
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China,Sichuan Translational Medicine Research Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Xiaoyan Tao
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China,Sichuan Translational Medicine Research Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Li Jiang
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China,Sichuan Translational Medicine Research Hospital, Chinese Academy of Sciences, Chengdu, China,*Correspondence: Li Jiang, ; Jie Zhang,
| | - Jie Zhang
- Department of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China,Sichuan Translational Medicine Research Hospital, Chinese Academy of Sciences, Chengdu, China,*Correspondence: Li Jiang, ; Jie Zhang,
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24
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Zhang C, Lin Y, Huang C, Huang Z, Fang X, Bai G, Zhang Z, Li W, Zhang W. Metagenomic next-generation sequencing assists the diagnosis treatment of fungal osteoarticular infections. Front Cell Infect Microbiol 2022; 12:1072539. [PMID: 36506031 PMCID: PMC9726756 DOI: 10.3389/fcimb.2022.1072539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/03/2022] [Indexed: 11/24/2022] Open
Abstract
Background Fungal osteoarticular infection (FOI) is not commonly seen in clinical practice but proposes a great challenge to orthopedic surgeons. In this study, we aimed to investigate the risk factors, the clinical features, and surgical outcomes of FOI in our institution. Specifically, we aimed to explore the role of metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of FOI. Methods All the patients who were diagnosed and managed with FOI in our institution from January 2007 to December 2020 were retrospectively reviewed, including primary fungal implant-related infection, primary fungal osteomyelitis or arthritis, and fungal infections secondary to bacterial osteomyelitis or implant-related bacterial infections. The potential risk factors and the clinical and surgical features were analyzed. The pathogen data were compared between culture and the mNGS test. Results A total of 25 patients were included, namely, 12 primary implant-related infections, 7 primary fungal osteomyelitis or arthritis, and 6 fungal infections secondary to bacterial osteomyelitis or implant-related bacterial infections. Most cases had undergone multiple surgeries or long-term antibiotic treatment. Diagnosis was mainly based on microbial culture and the mNGS test. Optimization of culture methods and the use of mNGS assisted the diagnosis. Specifically, mNGS was performed in 12 patients, 5 of whom were culture-negative. In the remaining seven cases, mNGS demonstrated the same results as culture. Management of FOI was complicated as most patients required multiple surgeries followed by long-term antifungal treatment. In selected cases, antifungal-impregnated cement spacer retention can be an optional choice. The overall success rate was 100% (25/25) for our cohort. Conclusion We concluded that patients with comorbidities and a history of multiple surgeries or long-term antibiotics are under higher risk for FOI. Use of mNGS assists the diagnosis and treatment of FOI. Surgery combined with long-term antifungal treatment achieved satisfactory outcomes. In selected cases, antifungal-impregnated cement spacer retention can be an optional treatment choice.
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Affiliation(s)
- Chaofan Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yunzhi Lin
- Department of Stomatology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Stomatology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Changyu Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xinyu Fang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Guochang Bai
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zeyu Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,*Correspondence: Wenming Zhang,
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Wang H, Yan S, Liu Y, Li Y, Cui G, Ma X. Metagenomic next-generation sequencing assists in the diagnosis of Cryptococcus pneumonia: Case series and literature review. Front Public Health 2022; 10:971511. [PMID: 36408040 PMCID: PMC9672815 DOI: 10.3389/fpubh.2022.971511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background Pulmonary cryptococcosis (PC) was once thought to occur only in patients with immune deficiencies, such as tested positive for the Human Immunodeficiency Virus (HIV). However, in recent years, it has been discovered that more than half of the patients with PC in our nation are individuals with normal immune function. As more and more PC cases are recorded, our diagnosis and treatment approaches, as well as our understanding of PC, are gradually improving. In reality, most PC patients still have a high incidence of misdiagnosis on their initial visit. It is primarily linked to the diverse clinical manifestations, atypical imaging findings, and inaccurate diagnostic approaches. Methods The research was conducted from 2019 to 2020. We performed traditional microbiological testing and mNGS on sample from patients with fever of Pulmonary nodules or lung infections. Furthermore, we collected patients' baseline information, clinical features, laboratory and imaging examination results, diagnosis, treatment and outcome. In the end, we confirmed three cases of PC using biopsy and mNGS. Conclusion Our data demonstrates that mNGS can be utilized as an auxiliary method for PC diagnosis. Early mNGS aids in the identification of pathogens, enabling early diagnosis and treatment, as well as a reduction in the rate of misdiagnosis and illness progression.
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Affiliation(s)
- Huifen Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Su Yan
- Health Management Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, 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, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangying Cui
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Guangying Cui
| | - Xiaoxu Ma
- Department of Respiratory Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Xiaoxu Ma
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Deng W, Xu H, Wu Y, Li J. Diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in pediatric pneumonia. Front Cell Infect Microbiol 2022; 12:950531. [PMID: 36389175 PMCID: PMC9648200 DOI: 10.3389/fcimb.2022.950531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/26/2022] [Indexed: 07/25/2023] Open
Abstract
OBJECTIVES The aim of this study was to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) versus conventional microbiological tests (CMTs) for pediatric pneumonia. METHODS This retrospective observational study enrolled 103 children who were diagnosed with pneumonia and hospitalized at Hubei Maternity and Child Health Care Hospital between 15 October 2020 and 15 February 2022. The pneumonia diagnosis was based on clinical manifestations, lung imaging, and microbiological tests. Pathogens in the lower respiratory tract were detected using CMTs and BALF mNGS (of DNA and RNA). The diagnostic performance of BALF mNGS was compared with that of CMTs. RESULTS In 96 patients, pathogens were identified by microbiological tests. The overall pathogen detection rate of mNGS was significantly higher than that of CMTs (91.3% vs. 59.2%, p = 0.000). The diagnostic performance of mNGS varied for different pathogens; however, its sensitivity and accuracy for diagnosing bacterial and viral infections were both higher than those of CMTs (p = 0.000). For the diagnosis of fungi, the sensitivity of mNGS (87.5%) was higher than that of CMTs (25%); however, its specificity and accuracy were lower than those of CMTs (p < 0.01). For the diagnosis of Mycoplasma pneumoniae, the specificity (98.8%) and accuracy (88.3%) of mNGS were high; however, its sensitivity (42.1%) was significantly lower than that of CMTs (100%) (p = 0.001). In 96 patients with definite pathogens, 52 cases (50.5%) were infected with a single pathogen, while 44 cases (42.7%) had polymicrobial infections. Virus-bacteria and virus-virus co-infections were the most common. Staphylococcus aureus, Haemophilus influenzae, rhinovirus, cytomegalovirus, parainfluenza virus, and fungi were more likely to be associated with polymicrobial infections. CONCLUSIONS BALF mNGS improved the detection rate of pediatric pneumonia, especially in mixed infections. The diagnostic performance of BALF mNGS varies according to pathogen type. mNGS can be used to supplement CMTs. A combination of mNGS and CMTs may be the best diagnostic strategy.
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Affiliation(s)
- Wenhua Deng
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Huan Xu
- Department of Scientific Affairs, Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Yabin Wu
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Jie Li
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
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Zhang Y, Chen J, Yi X, Chen Z, Yao T, Tang Z, Zang G, Cao X, Lian X, Chen X. Evaluation of the metagenomic next-generation sequencing performance in pathogenic detection in patients with spinal infection. Front Cell Infect Microbiol 2022; 12:967584. [PMID: 36389162 PMCID: PMC9646980 DOI: 10.3389/fcimb.2022.967584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/03/2022] [Indexed: 12/01/2023] Open
Abstract
Spinal infection is a rarely occurred pathology, whose diagnosis remains a major challenge due to the low sensitivity of culturing techniques. Metagenomic next-generation sequencing (mNGS) is a novel approach to identify the pathogenic organisms in infectious diseases. In this study, mNGS technology was adopted for pathogenic detection in spinal infection from the tissue and pus samples. Additionally, the diagnostic performance of mNGS for spinal infection was evaluated, by comparing it with that of the conventional microbial culture, with the histopathological results as the gold standard. Overall, 56 samples from 38 patients were enrolled for mNGS testing, and 69 samples were included for microbial culture. 30 patients (78.95%) were identified to be positive by the mNGS method, which was higher than that of microbial culture (17, 44.74%). The sensitivity and specificity of mNGS with pus samples were 84.2% and 100.0%, respectively, which outperformed those of microbial culture (42.1% and 100.0%). The pathogen identification results were applied to medication guidance, and all 38 patients experienced favorable outcomes at three months, followed-up post-treatment, without any adverse effects. These findings proved that mNGS was superior to microbial culture in pathogenic identification of the spinal infection, thereby showing great promise in guiding drug administration and improving clinical outcomes.
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Affiliation(s)
- Yi Zhang
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Jinmei Chen
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xiaoli Yi
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Zhiheng Chen
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Ting Yao
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Zhenghao Tang
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Guoqing Zang
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xuejie Cao
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Xiaofeng Lian
- Department of Orthopedics, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Xiaohua Chen
- Department of Infectious Diseases, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
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Yang A, Chen C, Hu Y, Zheng G, Chen P, Xie Z, Fan H, Sun Y, Wu P, Jiang W, Wang C, Zhang J, Zhang D, Wang J, Hu X, Xia H, Yin G, Guo Y. Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of Children. Microbiol Spectr 2022; 10:e0148822. [PMID: 36169415 DOI: 10.1128/spectrum.01488-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pneumonia is the leading cause of death in children; the pathogens are often difficult to diagnose. In this study, the performance of metagenomic next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from 112 children with confirmed pneumonia has been evaluated. mNGS performed a significantly higher positive detection rate (91.07%, 95% confidence interval [CI] 83.80% to 95.40%) and coincidence rate against the final diagnosis (72.32%, 95% CI 62.93% to 80.15%) than that of conventional methods (70.54%, 95% CI 61.06% to 78.58% and 56.25%, 95% CI 46.57% to 65.50%, respectively) (P < 0.01 and P < 0.05, respectively). Bacteria, viruses, and their mixed infections were common in children with pneumonia. Streptococcus pneumoniae was the most common bacterial pathogen in children with pneumonia, while Haemophilus parainfluenzae and Haemophilus influenzae seemed more likely to cause nonsevere pneumonia in children. In contrast, human cytomegalovirus (CMV) infection and the simultaneous bacterial infections could cause severe pneumonia, especially in children with underlying diseases. After adjustments of antibiotics based on mNGS and conventional methods, the conditions improved in 109 (97.32%) children. mNGS of BALF samples has shown great advantages in diagnosing the pathogenic etiology of pneumonia in children, especially when considering the limited volumes of BALF and the previous use of empirical antibiotics, contributing to the timely adjustment of antibiotic treatments, which can potentially improve the prognosis and decrease the mortality. IMPORTANCE Our study indicates high efficiency of mNGS using BALF for the detection of causative pathogens that cause pneumonia in children. mNGS can be a potential diagnostic tool to supplement conventional methods for children's pneumonia.
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Huang J, Wang L, Xu Y, Hu X, Yu R, Chen S, Wang B. Empyema caused by Eikenella halliae diagnosed by metagenomic next-generation sequencing (mNGS) after pulmonary surgery: A case report. Front Public Health 2022; 10:897602. [PMID: 36225772 PMCID: PMC9550235 DOI: 10.3389/fpubh.2022.897602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/31/2022] [Indexed: 01/22/2023] Open
Abstract
Background Empyema is one of the complications of pulmonary surgery for lung cancer, the incidence of which is not very high, but in severe cases, it can even lead to death, and it is always difficult to diagnose the cause by conventional methods. Case presentation In this study, we report a clinical case of empyema caused by Eikenella halliae after pulmonary surgery in a 55-year-old man. He had a fever, cough, and expectoration for 3 days and was diagnosed with right hydropneumothorax and empyema, pneumonia, postoperative malignant tumor of the right lower lobe (adenocarcinoma), and hypertension. The microbiology laboratory reported Gram-negative bacteria in pleural effusion, which was preliminarily considered as Eikenella based on culture and 16S rRNA sequencing. Furthermore, metagenomic next-generation sequencing (mNGS) of sputum samples was performed two times and reported negative results and the presence of E. halliae, respectively. The pathogen was finally confirmed as E. halliae by whole genome sequencing, suggesting the high-resolution ability of mNGS in the clinical diagnosis of this case. Conclusion To our knowledge, this is the first case report of E. halliae infection in China, indicating increased pathogenicity of Eikenella sp. in immunocompromised patients, especially after invasive operations. Our findings emphasize that mNGS allows bacterial diagnosis of empyema and can significantly improve the accuracy of the diagnosis.
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Affiliation(s)
- Jie Huang
- Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
| | - Liming Wang
- Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
| | - Yumei Xu
- Department of Microbiology Laboratory, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
| | - Xinhua Hu
- Department of Critical Medicine, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
| | - Ronghuan Yu
- Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
| | - Shi Chen
- Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Jianghan University, Wuhan, China
| | - Baoqing Wang
- Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China,Department Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China,*Correspondence: Baoqing Wang
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Yan H, Li Z, Xia H, Li Q, Bai H. A case report on mixed pulmonary infection of Nocardia nova, Mycobacterium tuberculosis, and Aspergillus fumigatus based on metagenomic next-generation sequencing. Front Public Health 2022; 10:927338. [PMID: 36148364 PMCID: PMC9485662 DOI: 10.3389/fpubh.2022.927338] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/29/2022] [Indexed: 01/24/2023] Open
Abstract
Background Pulmonary infection is one of the common complications of long-term use of glucocorticoids. Severe infections not only increase the length of hospital stay and treatment costs but also cause progression or recurrence of the primary disease. Case description Herein, we reported a case of mixed pulmonary infection secondary to glucocorticoid use. Rare pathogens such as Nocardia nova, Mycobacterium tuberculosis, Aspergillus fumigatus, and cytomegalovirus were detected by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and lung puncture tissue. Combining the results of conventional pathogen detection and clinical symptoms, the patient was diagnosed with mixed pulmonary infection by multiple pathogens. After timely targeted medication, the patient was finally discharged with a good prognosis. Conclusion To our knowledge, this is the first case report on mixed pulmonary infection with pathogens including Nocardia nova, Mycobacterium tuberculosis, Aspergillus fumigatus, and human cytomegalovirus. As a new clinical diagnostic method, mNGS has great advantages in diagnosis of diseases such as mixed infections.
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Affiliation(s)
- Haiming Yan
- Department of Infectious Diseases, The First People's Hospital of Foshan, Foshan, China
| | - Zhandong Li
- Department of Infectious Diseases, The First People's Hospital of Foshan, Foshan, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Qixin Li
- Department of Laboratory, The First People's Hospital of Foshan, Foshan, China,Qixin Li
| | - Honglian Bai
- Department of Infectious Diseases, The First People's Hospital of Foshan, Foshan, China,*Correspondence: Honglian Bai
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Wang J, Xu D, Qu B, Geng C. Adult intracranial infection caused by an extended-spectrum-beta-lactamase-producing strain of hypervirulent Klebsiella pneumoniae: a case report. Ann Transl Med 2022; 10:941. [PMID: 36172112 PMCID: PMC9511199 DOI: 10.21037/atm-22-3805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022]
Abstract
Background Klebsiella pneumoniae is a conditional pathogen related to several infectious diseases. Few studies reported Klebsiella pneumoniae meningitis in the Chinese population, guidelines on diagnosis and treatment of Klebsiella pneumoniae meningitis should be considered due to its high lethality. Here, we report a case of adult intracranial infection caused by extended-spectrum-beta-lactamase (ESBL)-producing hypervirulent Klebsiella pneumoniae (hvKP) in a 65-year-old female, providing new insight for clinical awareness and epidemiological surveillance for ESBL-producing hvKP infection. Case Description A 65-year-old female who had a recurrent fever for more than 1 month, and vomiting for 1 week was admitted to our hospital. The computed tomography (CT) results and laboratory results indicated systematic infection, and the blood culture confirmed the infection of Klebsiella pneumoniae. A combination of antibiotics including vancomycin, caspofungin, dexamethasone, and posaconazole oral suspension was given to the patient. Further, she exhibited a convulsion with unconsciousness, the CT revealed lacunar infarction and encephalomalacia. The following physical examination showed slight neck resistance, a weak light response of the eye, low muscle tension, suspicious left Babinski sign (+), and right Babinski sign (−). The CT and cerebrospinal fluid (CSF) analyses confirmed the diagnosis of intracranial infection caused by Klebsiella pneumoniae. We employed CSF microbial metagenomic next-generation sequencing (mNGS) was employed and the results suggested the high sequence of Klebsiella pneumoniae with drug-resistant gene SHV-type beta-lactamases (blaSHV). Subsequently, 2 g meropenem every 8 hours (q8h) prolonged for 3 hours was applied to treat intracranial infection, and her body temperature and infectious manifestations were gradually relieved. The CT results represented that pulmonary edema and pleural effusion were gradually dissipated and absorbed. Based on the improvement of clinical manifestations, the patient was discharged from the hospital and a close follow-up was conducted. Conclusions An ESBL-producing strain of hvKP could lead to invasive infection such as severe intracranial infection, with a relatively favorable prognosis. The outcome of the disease caused by Klebsiella pneumoniae infection is firmly related to the phenotypic features, for instance, virulence factors and antibiotic susceptibility. Due to its high lethality, timely empiric anti-infection therapy and close surveillance are necessary for patients with Klebsiella pneumoniae infection in the clinic.
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Affiliation(s)
- Junyu Wang
- Department of Pharmacy, The Affiliated Qingdao Central Hospital of Qingdao University, Qingdao, China
| | - Dexiang Xu
- Department of Pharmacy, The Affiliated Qingdao Central Hospital of Qingdao University, Qingdao, China
| | - Binbin Qu
- Department of Pharmacy, The Affiliated Qingdao Central Hospital of Qingdao University, Qingdao, China
| | - Chuanxin Geng
- Department of Pharmacy, The Affiliated Qingdao Central Hospital of Qingdao University, Qingdao, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Duan W, Yang Y, Zhao J, Yan T, Tian X. Application of metagenomic next-generation sequencing in the diagnosis and treatment of recurrent urinary tract infection in kidney transplant recipients. Front Public Health 2022; 10:901549. [PMID: 36072369 PMCID: PMC9441654 DOI: 10.3389/fpubh.2022.901549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/12/2022] [Indexed: 01/22/2023] Open
Abstract
Background Rapid and accurate pathogen diagnosis is an urgent unmet clinical need for recurrent urinary tract infection (RUTI) in kidney transplant recipients (KTRs). Metagenomic next-generation sequencing (mNGS) may offer another strategy for diagnosing uropathogens but remains to be studied. Methods Nineteen KTRs with RUTI were collected in this study. The uropathogens were detected and compared by mNGS and urine culture, respectively. Modifications of the anti-infection strategy were also assessed. Results Rich and diverse pathogens were revealed by mNGS. mNGS was significantly higher than culture in total positive rate (100.0% vs. 31.6%; p < 0.01) and in identification rates for bacteria (89.5% vs. 31.6%; p < 0.01), for viruses (57.9% vs. 0; p < 0.01), and for fungi (42.1% vs. 0; p < 0.01), respectively. mNGS identified a significantly higher proportion of mixed infections than culture (89.5% vs. 10.5%; p < 0.01). The anti-infection therapies were adjusted in two (33.3%) and 12 (76.9%) cases guided by culture and mNGS, respectively. Conclusion mNGS has more remarkable etiological diagnostic performance compared with urine culture for KTRs with RUTI to guide anti-infection strategies and, in turn, protect the graft.
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Affiliation(s)
- Wenjing Duan
- Department of the Clinical Research Center, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Yongguang Yang
- Department of the Clinical Research Center, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Jingge Zhao
- Department of the Clinical Research Center, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China
| | - Tianzhong Yan
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China,Tianzhong Yan
| | - Xiangyong Tian
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, China,*Correspondence: Xiangyong Tian
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Gu M, Mo X, Tang Z, Tang J, Wang W. Case Report: Diagnosis of Acute Q Fever With Aseptic Meningitis in a Patient by Using Metagenomic Next-Generation Sequencing. Front Med (Lausanne) 2022; 9:855020. [PMID: 35665349 PMCID: PMC9157756 DOI: 10.3389/fmed.2022.855020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022] Open
Abstract
Query fever (Q fever) is a widespread zoonotic disease caused by the bacterium of Coxiella burnetii (C. burnetii). Its neurological complications are rarely reported. But they may lead to severe consequences. It needs a rapid and accurate detective method to diagnose acute Q fever with neurological presentations in non-epidemic areas urgently. Here, we report an acute Q fever case with aseptic meningitis. The male patient, without any contact history in the epidemic area or with animals, was indicated to exhibit fever and headache symptoms. The cultures of blood, stool, urine, and sputum were all negative. But C. burnetii was repeatedly detected in blood by metagenomic next-generation sequencing (mNGS). He received Doxycycline therapy and quickly returned to normal. Therefore, for the diagnosis and identification of Q fever in non-reporting regions, mNGS has comparative advantages. Secondly, aseptic meningitis may be a direct infection of C. burnetii to central nervous system (CNS) or inflammatory reactions to systemic infection, we recommend detecting mNGS both in blood and cerebrospinal fluid (CSF).
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Affiliation(s)
- Meifeng Gu
- Department of Neurology, the Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoqin Mo
- Department of Neurology, the Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhenchu Tang
- Department of Neurology, the Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, the Second Xiangya Hospital, Central South University, Changsha, China
| | - Jianguang Tang
- Department of Neurology, the Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Wang
- Department of Neurology, the Second Xiangya Hospital, Central South University, Changsha, China
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Wang M, Liu W, Xiong Z, Li Z, Li J, Xu X, Zhang M, Xing M, Ning Q, Wu D, Qi J. Case Report: "Area of Focus" Atypical Trichinellosis and Fascioliasis Coinfection. Front Med (Lausanne) 2022; 9:881356. [PMID: 35646994 PMCID: PMC9132012 DOI: 10.3389/fmed.2022.881356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/19/2022] [Indexed: 11/21/2022] Open
Abstract
Parasitic co-infection is commonly observed in natural populations, yet rare in the laboratory. Multiparasitism can have negative effects on the host, ranging from the atypical manifestations to increased mortality, consequently, it may be misdiagnosed and treated with unsuitable anthelmintic medicines. Therefore, reliable diagnosis is critical for appropriate treatment of parasitic co-infection. Herein, we report a case of a 31-year-old woman with persistent eosinophilia and hypoechoic liver lesion on ultrasound. The microscopic examination of multiple stool specimens did not find any pathogens. The patient had serum specific anti-Trichinella IgG antibody by Dot enzyme-linked immunosorbent assay (Dot-ELISA). After treatment with albendazole, contrast-enhanced magnetic resonance imaging (MRI) revealed more lesions in the liver. Subsequently, liver biopsy was performed in this patient and Fasciola hepatica was identified using metagenomic next-generation sequencing (mNGS) as well as polymerase chain reaction. After treatment with triclabendazole, which is the only anthelmintic drug specifically available against this fluke, her eosinophil count returned normal, and the liver lesions were significantly regressed. This case highlights the diagnostic challenge posed by parasitic co-infection, which merits more in-depth evaluation to confirm the diagnosis.
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Affiliation(s)
- Meng Wang
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Liu
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ziman Xiong
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhen Li
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiansha Li
- Department of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Xu
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Zhang
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingyou Xing
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Ning
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Di Wu
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junying Qi
- National Medical Center for Major Public Health Events, Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Li J, Zhang Y, Zhang Q, Lu S, Huang F, Wang J. Application of metagenomic next-generation sequencing for the diagnosis of intracranial infection of Listeria monocytogenes. Ann Transl Med 2022; 10:672. [PMID: 35845529 PMCID: PMC9279819 DOI: 10.21037/atm-22-2186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/31/2022] [Indexed: 11/24/2022]
Abstract
Background Intracranial infection of Listeria monocytogenes (LM) can lead to various manifestations, including meningitis, meningoencephalitis, brainstem encephalitis, and brain abscess, which often have a poor prognosis. Metagenomic next-generation sequencing (mNGS) is a promising new tool for the diagnosis of intracranial infection of LM. We describe the typical clinical manifestations of LM intracranial infection and highlight its rarity and severity to help physicians better understand the disease characteristics. Methods Six cases of severe LM intracranial infection were diagnosed by mNGS. We conducted a retrospective analysis of the data on disease progression, diagnostic tools, treatments, and outcomes, and summarized the findings. We compared the differences in diagnostic accuracy and timeliness between mNGS and etiological cultures. Results Among the 6 patients, 5 were males and 1 was female (age range 32–83). Three patients had a history of immunosuppressive therapy. Common symptoms included fever (100%) and a stiff neck (100%). Coma occurred early in severe patients (66%). Two healthy young patients had previously developed with meningitis, while coma occurred in 3 immunosuppressed patients and 1 elderly patient. Three immunosuppressed patients presented with brain abscess, brainstem encephalitis, and meningitis. 1 elderly patient presented with meningitis. Two patients developed septic shock complications early. Laboratory data showed normal or slightly increased leukocytes, neutrophils, and procalcitonin, and cerebrospinal fluid (CSF) tests were consistent with bacterial CSF infection. All 6 patients were examined for blood culture and CSF culture. The positive rate of blood culture and CSF culture was 50% and 16%. The average time from admission to positive culture findings was 91 h. All 6 patients were examined for CSF mNGS. Two were also examined for whole-blood mNGS. The positive rate for CSF mNGS and whole-blood mNGS results was 100%. The mean time from admission to positive mNGS report was 47 h. After diagnosis and treatment with sensitive antibiotics, 1 patient with brain abscess developed neurological sequelae, while the other 5 patients completely recovered. Conclusions mNGS can improve accuracy in the diagnosis of LM intracranial infection and reduce the delay in diagnosis. Intracranial infection of Listeria monocytogenes responds well to the timely use of appropriate antibiotics.
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Affiliation(s)
- Jing Li
- Department of Intensive Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - You Zhang
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Quanquan Zhang
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Shiqi Lu
- Department of Intensive Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fang Huang
- Department of Intensive Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Wang
- Department of Intensive Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
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Zhang J, Luo J, Weng X, Zhu Y, Goyal G, Perna F, Espinoza-Gutarra M, Jiang L, Chen L, Mi JQ. A case report of the metagenomics next-generation sequencing for early detection of central nervous system mucormycosis with successful rescue in patient with recurrent chronic lymphocytic leukemia. Ann Transl Med 2022; 10:722. [PMID: 35845522 PMCID: PMC9279813 DOI: 10.21037/atm-22-2533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/20/2022] [Indexed: 11/06/2022]
Abstract
Background Central nervous system (CNS) mucormycosis is insidious and difficult to diagnose. It progresses rapidly and causes high mortality. Rare cases have been reported during ibrutinib use, which have poor prognosis. Through this case, we share the experience of successful diagnosis and treatment. We also emphasize the importance of focusing on high-risk groups, early diagnosis and prompt management. Case Description In this case, a 52-year-old patient was diagnosed with chronic lymphocytic leukemia (CLL) for more than 5 years. He was in remission after rituximab plus fludarabine and cyclophosphamide (RFC) regimen, and relapsed in the fourth year. During the ibrutinib monotherapy, the patient presented with sudden headache. Cranial imaging examination revealed a definite right occipitoparietal lobe mass with extensive edema. A rapid diagnosis of mucormycosis infection was made using metagenomic next-generation sequencing (mNGS). The patient at that time didn't have neutropenia, but he had hypogammaglobulinemia. The infection was treated with amphotericin B cholesteryl sulfate complex, posaconazole, and interventional surgery, and the treatment was successful. At the same time, we considered the control of disease progression in this relapsed patient with, as well as to the drug interaction with posaconazole. We chose the next generation Bruton's tyrosine kinase (BTK) inhibitor zanubrutinib as the treatment, whose safety has been identified. As of the submission date, the patient has been followed up for nearly 1 year, and his disease is stable. Conclusions When new clinical problems arise in recurrent CLL patients, it is important to identify multiple factors, especially the insidious fungal infections. In particular, the immunocompromised patients should be concerned. CNS mucormycosis is extremely deadly, the early diagnosis will improve the prognosis. In clinical practice, the gold standard diagnosis of mucormycosis is difficult to obtain through pathology. In this case, mNGS was applied to quickly diagnose mucormycosis, enabling earlier treatment and ameliorating the prognosis. Thus, it will help us to early detect this group of people who may be potentially infected. Current guidelines do not recommend the prophylactic use of antifungal agents in treated CLL patients. However, in patients with prior severe infection or hypogammaglobulinemia, intravenous immunoglobulin is recommended to reduce the associated infection rate.
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Affiliation(s)
- Jiaojiao Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Luo
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangqin Weng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongmei Zhu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Gaurav Goyal
- Division of Hematology and Oncology, University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
| | - Fabiana Perna
- Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Manuel Espinoza-Gutarra
- Division of Hematology/Oncology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Lu Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian-Qing Mi
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Chen H, Zhang Y, Zheng J, Shi L, He Y, Niu Y, Lei J, Zhao Y, Xia H, Chen T. Application of mNGS in the Etiological Diagnosis of Thoracic and Abdominal Infection in Patients With End-Stage Liver Disease. Front Cell Infect Microbiol 2022; 11:741220. [PMID: 35071029 PMCID: PMC8766839 DOI: 10.3389/fcimb.2021.741220] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
Background Despite the obvious advantages of metagenomic next-generation sequencing (mNGS) in etiological diagnosis of various infectious diseases, there are few reports on etiological diagnosis of suspected thoracic and abdominal infections in patients with end-stage liver disease (ESLD). Methods Seventy-three ESLD patients were enrolled from January 2019 to May 2021 due to suspected complicated thoracic and abdominal infections with poor response to empirical anti-infective treatment. Pleural effusion and ascites samples of these patients were collected for mNGS detection and conventional pathogen culture. The application value of mNGS in etiological diagnosis of thoracic and abdominal infections in ESLD patients was finally evaluated. Results A total of 96 pathogens were detected using mNGS method, including 47 bacteria, 32 viruses, 14 fungi, 2 Mycobacterium tuberculosis, and 1 parasite. The positive rate of mNGS reached 42.5%, which was significantly higher than that of conventional culture method (21.9%) (p = 0.008). Considering neutrophil counts, the overall positive rate of bacteria detection of both methods in Polymorphonuclear Neutrophils (PMN) ≥250/mm3 group was 64.3% and in PMN <250/mm3 group was 23.7%. Compared with the final clinical diagnosis, the agreement rate of mNGS in patients with positive bacteria detection and with suspected positive bacteria detection was 78.6% (11/14) and 44.4% (8/18), respectively. In addition, the agreement rate of mNGS was 66.7% (4/6, respectively) in patients with positive and suspected fungal detection. Interestingly, of the 11 patients with fungal detection, 5 had alcoholic liver disease, accounting for 45.5% of all patients with alcoholic liver disease. We also detected 32 strains of viruses using mNGS, mainly cytomegalovirus (62.5%). Conclusions The mNGS method is a useful supplement to conventional culture methods, which performs a higher positive rate, higher sensitivity, and broader pathogen spectrum, especially for rare pathogens and those difficult to culture. For ESLD patients, mNGS has great prospects in early etiological diagnosis of thoracic and abdominal infections. In addition, the cutoff values for the diagnosis of bacterial infection (PMN ≥250/mm3) in the thoracic and abdominal cavities may need to be redefined.
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Affiliation(s)
- Hongmei Chen
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ye Zhang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Jie Zheng
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lei Shi
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yingli He
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yinghua Niu
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jine Lei
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yingren Zhao
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Tianyan Chen
- Department of Infectious Diseases, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Du Y, Zhang Z, Chen C, Xia H, Zhang H, Guo Z, Wang Y. Case Report: Report of Infective Endocarditis Caused by Abiotrophia defectiva and Literature Review. Front Pediatr 2022; 10:894049. [PMID: 35874573 PMCID: PMC9299070 DOI: 10.3389/fped.2022.894049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE To report the clinical features of the first child with infective endocarditis (IE) caused by Abiotrophia defectiva in mainland China and to raise awareness of the disease. METHODS The clinical data of a child with IE caused by A. defectiva admitted to Xi'an Children's Hospital in July 2021 were collected, and the relevant literature was reviewed. RESULTS The child was a female, 8 years old, admitted with fever for 4 days and right-sided limb weakness for 3 days. The illness started with suppurative tonsillitis, followed by headache, fatigue, right-sided mouth, slurred speech, right limb weakness, and unstable holding. Transthoracic echocardiography showed that the mitral valve vegetation was formed and vegetation could also be seen at the entrance of the pulmonary vein at the posterior wall of the left atrium. Cranial contrast-enhanced MRI + magnetic resonance angiography showed multiple intracranial pseudoaneurysm formation and pontine infarction. After A. defectiva was detected by metagenomic next-generation sequencing (mNGS) in cerebrospinal fluid and blood detected, the infection was controlled by anti-infective treatment with meropenem and vancomycin. On the 36th day after admission, due to severe headache and slurred speech, the head CT showed hemorrhage of right parietal pseudoaneurysm and cerebral sickle hernia, and right temporo-occipital hematoma evacuation, cerebrovascular malformation resection, and cranial decompression were performed immediately. After the surgery, her speech ability gradually recovered, the muscle strength of her left upper limb was about grade III, while the muscle strength of the rest of the limbs was normal. After a total of 60 days of hospitalization, her family requested to be discharged. CONCLUSION This pediatric patient is the first case of childhood IE caused by A. defectiva in mainland China, and the first time in the world that A. defectiva was detected by mNGS in patients with IE.
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Affiliation(s)
- Yanqiang Du
- Department of Pediatric Intensive Care Unit of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Zhan Zhang
- Department of Ultrasound of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Chao Chen
- Imaging Department of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Han Xia
- Hugobiotech Co., Ltd., Beijing, China
| | - Hua Zhang
- Department of Pediatric Intensive Care Unit of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Zhangyan Guo
- Department of Pediatric Intensive Care Unit of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yi Wang
- Department of Pediatric Intensive Care Unit of Xi'an Children's Hospital, National Children's Regional Medical Center (Northwest), Children's Hospital, Xi'an Jiaotong University, Xi'an, China
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Zhang Y, Xu H, Liu Y, Kang J, Chen H, Wang Z, Cai D. Case Report: Fascioliasis Hepatica Precisely Diagnosed by Metagenomic Next-Generation Sequencing and Treated With Albendazole. Front Med (Lausanne) 2021; 8:773145. [PMID: 34901089 PMCID: PMC8651557 DOI: 10.3389/fmed.2021.773145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
The clinical manifestations of fascioliasis hepatica in humans are unspecific. Traditional diagnosis relies on evidence of live parasites or eggs in the bile or feces. However, due to similar imaging manifestations, they are often misdiagnosed as malignant tumors. Here, we report a case of a 43-year-old woman with fever and space-occupying liver disease. Liver biopsy, parasite-specific antibody screening, and stool testing did not find any pathogens. Therefore, metagenomic next-generation sequencing (mNGS) and routine microbiological examinations were performed. Finally, Fasciola hepatica was only identified by mNGS. The body temperature of the patient and the eosinophil count remained normal, and the space-occupying liver lesions were significantly absorbed after more than 7 months of treatment with albendazole. The details of this case highlight the timely use of mNGS to identify parasites and judge therapeutic effects after treatment, providing important help for clinical decision-making.
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Affiliation(s)
- Yaling Zhang
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Huan Xu
- Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Yi Liu
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Kang
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hairu Chen
- Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Zhiyi Wang
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dachuan Cai
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Jiang H, Wu C, Xu J, Wang Q, Shen L, Ou X, Liu H, Han X, Wang J, Ding W, Hu L, Chen X. Bacterial and Fungal Infections Promote the Bone Erosion Progression in Acquired Cholesteatoma Revealed by Metagenomic Next-Generation Sequencing. Front Microbiol 2021; 12:761111. [PMID: 34803987 PMCID: PMC8604023 DOI: 10.3389/fmicb.2021.761111] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/11/2021] [Indexed: 01/08/2023] Open
Abstract
An acquired cholesteatoma generally occurs as a consequence of otitis media and eustachian tube dysfunction. Patients with acquired cholesteatoma generally present with chronic otorrhea and progressive conductive hearing loss. There are many microbes reportedly associated with acquired cholesteatoma. However, conventional culture-based techniques show a typically low detection rate for various pathogenetic bacteria and fungi. Metagenomic next-generation sequencing (mNGS), an emerging powerful platform offering higher sensitivity and higher throughput for evaluating many samples at once, remains to be studied in acquired cholesteatoma. In this study, 16 consecutive patients from January 2020 to January 2021 at the Second Affiliated Hospital of Zhejiang University School of Medicine (SAHZU) were reviewed. We detected a total of 31 microbial species in patients, mNGS provided a higher detection rate compared to culture (100% vs. 31.25%, p = 0.000034). As the severity of the patient’s pathological condition worsens, the more complex types of microbes were identified. The most commonly detected microbial genus was Aspergillus (9/16, 56.25%), especially in patients suffering from severe bone erosion. In summary, mNGS improves the sensibility to identify pathogens of cholesteatoma patients, and Aspergillus infections increase bone destruction in acquired cholesteatoma.
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Affiliation(s)
- Hua Jiang
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengpeng Wu
- Eye Center of the Second Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingjie Xu
- Eye Center of the Second Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Wang
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lei Shen
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xunyan Ou
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongyan Liu
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xu Han
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Jun Wang
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Wenchao Ding
- Hangzhou Matridx Biotechnology Co., Ltd., Hangzhou, China
| | - Lidan Hu
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiangjun Chen
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Eye Center of the Second Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
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Shi L, Xia H, Moore MD, Deng C, Li N, Ren H, Chen Y, Liu J, Du F, Zheng G, Li J, Han Q, Fan W, Ye F, Lin S, Liu Z, Liu H, Wang Y, Yang J, Liu Q, Zhao Y, Chen T. Metagenomic Next-Generation Sequencing in the Diagnosis of HHV-1 Reactivation in a Critically Ill COVID-19 Patient: A Case Report. Front Med (Lausanne) 2021; 8:715519. [PMID: 34671616 PMCID: PMC8520926 DOI: 10.3389/fmed.2021.715519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/08/2021] [Indexed: 01/08/2023] Open
Abstract
Background: Secondary infections pose tremendous challenges in Coronavirus disease 2019 (COVID-19) treatment and are associated with higher mortality rates. Clinicians face of the challenge of diagnosing viral infections because of low sensitivity of available laboratory tests. Case Presentation: A 66-year-old woman initially manifested fever and shortness of breath. She was diagnosed as critically ill with COVID-19 using quantitative reverse transcription PCR (RT-qPCR) and treated with antiviral therapy, ventilator and extracorporeal membrane oxygenation (ECMO). However, after the condition was relatively stabled for a few days, the patient deteriorated with fever, frequent cough, increased airway secretions, and increased exudative lesions in the lower right lung on chest X-rays, showing the possibility of a newly acquired infection, though sputum bacterial and fungal cultures and smears showed negative results. Using metagenomic next-generation sequencing (mNGS), we identified a reactivation of latent human herpes virus type 1 (HHV-1) in the respiratory tract, blood and gastrointestinal tract, resulting in a worsened clinical course in a critically ill COVID-19 patient on ECMO. Anti-HHV-1 therapy guided by these sequencing results effectively decreased HHV-1 levels, and improved the patient's clinical condition. After 49 days on ECMO and 67 days on the ventilator, the 66-year-old patient recovered and was discharged. Conclusions: This case report demonstrates the potential value of mNGS for evidence-based treatment, and suggests that potential reactivation of latent viruses should be considered in critically ill COVID-19 patients.
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Affiliation(s)
- Lei Shi
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Han Xia
- Hugobiotech Beijing Co., Ltd., Beijing, China
| | - Matthew D Moore
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Chao Deng
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Na Li
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Hui Ren
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Yunru Chen
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Jinfeng Liu
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Fenjing Du
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Gezhi Zheng
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Jing Li
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Qunying Han
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Wanhu Fan
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Feng Ye
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Shumei Lin
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Zhengwen Liu
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Hongjuan Liu
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Yawen Wang
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Jian Yang
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Qingguang Liu
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Yingren Zhao
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
| | - Tianyan Chen
- The First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China
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Zeng S, Yan WQ, Wu XM, Zhang HN. Case Report: Diagnosis of Klebsiella pneumoniae Invasive Liver Abscess Syndrome With Purulent Meningitis in a Patient From Pathogen to Lesions. Front Med (Lausanne) 2021; 8:714916. [PMID: 34568372 PMCID: PMC8460774 DOI: 10.3389/fmed.2021.714916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
As a determinant human pathogen, Klebsiella pneumoniae is known to cause rare K. pneumoniae liver abscess syndrome (KLAS) which was more common in Asia in early-stage and reported increasingly outside Asia now. Patients with KLAS who have septic metastatic ocular or central nervous system (CNS) lesions are associated with high morbidity and mortality. Relatively infrequent adult community-acquired K. pneumoniae meningitis have been documented and most were with poor prognosis. In this paper, we reported a case of KLAS presenting purulent meningitis as disease onset. While negative results were obtained in the bacterial culture of CSF, blood, or liver pus, metagenomic next-generation sequencing (mNGS) of CSF, and blood samples which were synchronously performed demonstrated Klebsiella pneumoniae as the pathogenic microorganism (13,470 and 5,318 unique reads, respectively). The ultimately cured patient benefited from rapid pathogen diagnosis, early percutaneous drainage of the abscess, and prompt appropriate antibiotic administration. Our case highlights the importance of clinicians using mNGS for early pathogen diagnosis of this disease.
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Affiliation(s)
- Sheng Zeng
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei-Qian Yan
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiao-Mei Wu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Hai-Nan Zhang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
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44
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Li J, Chen C, Zou F, Liu L, Wang B, Kang H, Liu B, Wang S, Qin T. Diagnosing scrub typhus without eschar: a case report using metagenomic next-generation sequencing (mNGS). Ann Transl Med 2021; 9:1190. [PMID: 34430631 PMCID: PMC8350650 DOI: 10.21037/atm-21-3015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/07/2021] [Indexed: 11/06/2022]
Abstract
Scrub typhus is a disease caused by the bacteria, Orientia tsutsugamushi, which is spread to people through the bites of infected larval mites. Symptoms include eschar at the place of infection, as well as many flu-like symptoms, e.g., fever, headache, chills and skin rash. As eschar is the most typical symptom of scrub typhus, it is often used to diagnose the disease, but if a patient does not display an obvious eschar lesion, diagnosing the disease can prove to be difficult. To help improve the diagnoses of scrub typhus, metagenomic next-generation sequencing (mNGS) has been used as a new approach to identifying pathogens. Here, we report a 51-year-old patient who had unexplained fever for a week and was admitted to hospital with no obvious eschar on her body. Smears and cultures of blood and sputum samples were first performed, but all returned a negative result for scrub typhus. We then conducted a mNGS analysis of blood and sputum samples and were able to identify the pathogenic microbe. Subsequently, a total of 377 reads, as well as 12 unique reads of Orientia tsutsugamushi were detected in the patient's blood and sputum. Quantitative polymerase chain reaction (qPCR) results of blood samples further confirmed our mNGS detection, suggesting that the patient did indeed have scrub typhus. From these results, we determined that mNGS as a diagnostic tool provides a better method of identifying clinical febrile pathogens with atypical characteristics.
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Affiliation(s)
- Jie Li
- Department of Critical Care Medicine, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Changwen Chen
- Department of Critical Care Medicine, Guangdong Provincial People's Hospital Ganzhou Hospital, Ganzhou Municipal Hospital, Guangzhou, China
| | - Fangqiang Zou
- Department of Critical Care Medicine, Guangdong Provincial People's Hospital Ganzhou Hospital, Ganzhou Municipal Hospital, Guangzhou, China
| | - Lin Liu
- Department of Critical Care Medicine, Guangdong Provincial People's Hospital Ganzhou Hospital, Ganzhou Municipal Hospital, Guangzhou, China
| | - Baolong Wang
- Department of Critical Care Medicine, Guangdong Provincial People's Hospital Ganzhou Hospital, Ganzhou Municipal Hospital, Guangzhou, China
| | - Huan Kang
- Department of Critical Care Medicine, Guangdong Provincial People's Hospital Ganzhou Hospital, Ganzhou Municipal Hospital, Guangzhou, China
| | - Binsen Liu
- Department of Critical Care Medicine, People's Hospital of Shangyou County, Ganzhou, China
| | - Shouhong Wang
- Department of Critical Care Medicine, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Tiehe Qin
- Department of Critical Care Medicine, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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45
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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: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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46
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Chen Y, Feng W, Ye K, Guo L, Xia H, Guan Y, Chai L, Shi W, Zhai C, Wang J, Yan X, Wang Q, Zhang Q, Li C, Liu P, Li M. Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infectious Pathogens From Bronchoalveolar Lavage Samples. Front Cell Infect Microbiol 2021; 11:541092. [PMID: 33777827 PMCID: PMC7991794 DOI: 10.3389/fcimb.2021.541092] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection. In this study, we assessed the value of mNGS for bronchoalveolar lavage (BAL) samples in the diagnosis of pulmonary infections. Methods From February 2018 to April 2019, BAL samples were collected from 235 patients with suspected pulmonary infections. mNGS and microbial culture were performed to evaluate the effectiveness of mNGS in pulmonary infection diagnosis. Results We employed mNGS to evaluate the alpha diversity, results suggesting that patients with confirmed pathogens had a lower microbial diversity index compared to that of patients with uncertain pathogens. For the patients admitted to the respiratory intensive care unit (RICU) or on a ventilator, they experienced a lower diversity index than that of the patients in the general ward or not on a ventilator. In addition, mNGS of BAL had a diagnostic sensitivity of 88.89% and a specificity of 14.86% in pulmonary infection, with 21.16% positive predictive value (PPV) and 83.87% negative predictive value (NPV). When rare pathogens were excluded, the sensitivity of mNGS decreased to 73.33%, and the specificity increased to 41.71%. For patients in the simple pulmonary infection group and the immunocompromised group, the main infection types were bacterial infection (58.33%) and mixed-infection (43.18%). Furthermore, mNGS had an advantage over culture in describing polymicrobial ecosystem, demonstrating the microbial distribution and the dominant strains of the respiratory tract in patients with different underlying diseases. Conclusions The study indicated that mNGS of BAL samples could provide more accurate diagnostic information in pulmonary infections and demonstrate the changes of respiratory microbiome in different underlying diseases. This method might play an important role in the clinical use of antimicrobial agents in the future.
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Affiliation(s)
- Yuqian Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wei Feng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Kai Ye
- Ministry of Education Key Lab for Intelligent, Networks and Networks Security, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Li Guo
- Ministry of Education Key Lab for Intelligent, Networks and Networks Security, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Han Xia
- Department of Research and Development, Hugobiotech Co., Ltd., Beijing, China
| | - Yuanlin Guan
- Department of Research and Development, Hugobiotech Co., Ltd., Beijing, China
| | - Limin Chai
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wenhua Shi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Cui Zhai
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jian Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xin Yan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qingting Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qianqian Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Cong Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Pengtao Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Manxiang Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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47
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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: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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48
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Wang K, Li P, Lin Y, Chen H, Yang L, Li J, Zhang T, Chen Q, Li Z, Du X, Zhou Y, Li P, Wang H, Song H. Metagenomic Diagnosis for a Culture-Negative Sample From a Patient With Severe Pneumonia by Nanopore and Next-Generation Sequencing. Front Cell Infect Microbiol 2020; 10:182. [PMID: 32432051 PMCID: PMC7214676 DOI: 10.3389/fcimb.2020.00182] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/06/2020] [Indexed: 12/18/2022] Open
Abstract
Rapid and accurate etiologic diagnosis accelerates targeted antimicrobial therapy. Metagenomic analysis has played a critical role in pathogen identification. In this study, we leveraged the advantages of both the MinION and BGISEQ-500 platforms to make a bacteriologic diagnosis from a culture-negative lung tissue sample from an immunocompromised patient with severe pneumonia. Real-time nanopore sequencing rapidly identified Klebsiella pneumoniae by an 823 bp specific sequence within 1 min. Genomic analysis further identified bla SHV-12, bla KPC-2, bla TEM-1, bla CTX-M-65, and other resistance genes. The same sample was further sequenced on the BGISEQ-500 platform, which presented consistent results regarding the most top dominant pathogens and provided additional information of resistance genes. Revised antibiotic treatment was followed by the patient's clinical recovery. Though sample preparation and the interpretation of final results still need to be improved further, metagenomic sequencing contributes to the accurate diagnosis of culture-negative infections and facilitates the rational antibiotic therapy.
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Affiliation(s)
- Kaiying Wang
- College of Military Medicine, Academy of Military Sciences, Beijing, China.,Center for Disease Control and Prevention of PLA, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Peihan Li
- College of Military Medicine, Academy of Military Sciences, Beijing, China.,Center for Disease Control and Prevention of PLA, Beijing, China
| | - Yanfeng Lin
- College of Military Medicine, Academy of Military Sciences, Beijing, China.,Center for Disease Control and Prevention of PLA, Beijing, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Lang Yang
- College of Military Medicine, Academy of Military Sciences, Beijing, China.,Center for Disease Control and Prevention of PLA, Beijing, China
| | - Jinhui Li
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Tingyan Zhang
- Center for Disease Control and Prevention of PLA, Beijing, China.,College of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, China
| | - Qichao Chen
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Zhonghong Li
- Center for Disease Control and Prevention of PLA, Beijing, China.,College of Environmental and Chemical Engineering, Nanchang Hangkong University, Nanchang, China
| | - Xinying Du
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Peng Li
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hongbin Song
- Center for Disease Control and Prevention of PLA, Beijing, China
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Abstract
Ureaplasma parvum (U. parvum) is common commensal in the female genitourinary tract. Despite U. parvum has been associated with chorioamnionitis, abortion, prematurity and perinatal complications, the invasive central nervous system (CNS) infection is rare in neonates. Diagnosis of U. parvum meningitis can be difficult for the atypical presentations and sterile cultures by conventional methods. Metagenomic next-generation sequencing (mNGS) could identify a broad range of human pathogens in a target-independent manner. Here, we performed mNGS to search for the infectious etiology in a term infant presenting with fever and seizure. U. parvum genome was identified by mNGS and further confirmed by PCR in the same cerebrospinal fluid (CSF) sample. As the quick and timely diagnosis, the baby was successfully treated with erythromycin for 4 weeks without complication. The clinical follow-up has showed that the physical and mental development are normal. In conclusion, mNGS may a promising diagnostic technology for U. parvum meningitis. As mNGS is able to identify diverse microbes in a single run, it could be a useful strategy to detection the clinical causative pathogens with atypical features in neonates.
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Affiliation(s)
- Qiu Wang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Kai Wang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Yuanbo Zhang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Chaosheng Lu
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Yana Yan
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xiaoxia Huang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Jing Zhou
- Department of Obstetrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Lijiang Chen
- Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Dan Wang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
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50
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Jin W, Miao Q, Wang M, Zhang Y, Ma Y, Huang Y, Wu H, Lin Y, Hu B, Pan J. A rare case of adrenal gland abscess due to anaerobes detected by metagenomic next-generation sequencing. Ann Transl Med 2020; 8:247. [PMID: 32309394 PMCID: PMC7154389 DOI: 10.21037/atm.2020.01.123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A 50-year-old woman presented with right back pain, low fever, leukocytosis, a high level of C-reactive protein and a high erythrocyte sedimentation rate. Abdominal magnetic resonance imaging (MRI) revealed a hypodense lesion in the right suprarenal region, while PET/CT showed mildly increased metabolic activity. A CT-guided percutaneous puncture was performed, and foul-smelling thick pus was removed, which indicated an anaerobic infection. A smear of the pus showed both gram-positive and gram-negative microorganisms. Traditional culture only detected Escherichia coli, Proteus mirabilis, and Actinomyces turicensis. While surprisingly, metagenomic next-generation sequencing (mNGS) of both the pus and blood showed high reads of multiple pathogens, including anaerobes and the three culture-positive pathogens. Thus, adrenal gland abscess was confirmed, and a combination therapy of catheter drainage and effective antimicrobial treatment was started. Six days later, the patient had clinically improved and mNGS showed dramatically decreased reads of all pathogens. A follow-up lab examination of inflammatory biomarkers was normal, and the adrenal mass was reduced radiographically.
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Affiliation(s)
- Wenting Jin
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qing Miao
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Mengran Wang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yao Zhang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yuyan Ma
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yingnan Huang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Honglong Wu
- Binhai Genomics Institute, Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Yang Lin
- BGI Genomics BGI-Shenzhen, Shenzhen 518083, China
| | - Bijie Hu
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China.,Department of Infectious Diseases and Department of Infection Control, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jue Pan
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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