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Liu Y, Wu W, Xiao Y, Zou H, Hao S, Jiang Y. Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients. Front Cell Infect Microbiol 2024; 14:1439472. [PMID: 39165919 PMCID: PMC11333343 DOI: 10.3389/fcimb.2024.1439472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/09/2024] [Indexed: 08/22/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) technology has been widely used to diagnose various infections. Based on the most common pathogen profiles, targeted mNGS (tNGS) using multiplex PCR has been developed to detect pathogens with predesigned primers in the panel, significantly improving sensitivity and reducing economic burden on patients. However, there are few studies on summarizing pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China on large scale. Methods From January 2021 to December 2023, bronchoalveolar lavage fluid (BALF) or sputum samples from 546 immunocompetent and immunocompromised patients with suspected community-acquired pneumonia were collected. Pathogen profiles in those patients on whom mNGS was performed were summarized. Additionally, we also evaluated the performance of tNGS in diagnosing pulmonary infections. Results Combined with results of mNGS and culture, we found that the most common bacterial pathogens were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii in both immunocompromised and immunocompetent patients with high detection rates of Staphylococcus aureus and Enterococcus faecium, respectively. For fungal pathogens, Pneumocystis jirovecii was commonly detected in patients, while fungal infections in immunocompetent patients were mainly caused by Candida albicans. Most of viral infections in patients were caused by Human betaherpesvirus 5 and Human gammaherpesvirus 4. It is worth noting that, compared with immunocompetent patients (34.9%, 76/218), more mixed infections were found in immunocompromised patients (37.8%, 14/37). Additionally, taking final comprehensive clinical diagnoses as reference standard, total coincidence rate of BALF tNGS (81.4%, 48/59) was much higher than that of BALF mNGS (40.0%, 112/280). Conclusions Our findings supplemented and classified the pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China. Most importantly, our findings can accelerate the development and design of tNGS specifically used for regional pulmonary infections.
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Affiliation(s)
- Yong Liu
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Wencai Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Yunping Xiao
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Hongyan Zou
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Sijia Hao
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Yanfang Jiang
- Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
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Liu M, Zhang H, Li L, Mao J, Li R, Yin J, Wu X. The etiological diagnostic value of metagenomic next-generation sequencing in suspected community-acquired pneumonia. BMC Infect Dis 2024; 24:626. [PMID: 38914949 PMCID: PMC11194883 DOI: 10.1186/s12879-024-09507-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/13/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND The emergence of metagenomic next-generation sequencing (mNGS) may provide a promising tool for early and comprehensive identification of the causative pathogen in community-acquired pneumonia (CAP). In this study, we aim to further evaluate the etiological diagnostic value of mNGS in suspected CAP. METHODS A total of 555 bronchoalveolar lavage fluid (BALF) samples were collected for pathogen detection by mNGS from 541 patients with suspected CAP. The clinical value was assessed based on infection diagnosis and treatment guidance. The diagnostic performance for pathogen identification by mNGS and sputum culture and for tuberculosis (TB) by mNGS and X-pert MTB/RIF were compared. To evaluate the potential for treatment guidance, we analyzed the treatment regimen of patients with suspected CAP, including imaging changes of lung after empirical antibacterial therapy, intensified regimen, antifungal treatment, and a 1-year follow up for patients with unconfirmed diagnosis and non-improvement imaging after anti-infective treatment and patients with high suspicion of TB or NTM infection who were transferred to the Wuhan Pulmonary Hospital for further diagnosis and even anti-mycobacterium therapy. RESULTS Of the 516 BALF samples that were analyzed by both mNGS and sputum culture, the positivity rate of mNGS was significantly higher than that of sputum culture (79.1% vs. 11.4%, P = 0.001). A total of 48 samples from patients with confirmed TB were analyzed by both mNGS and X-pert MTB/RIF, and the sensitivity of mNGS for the diagnosis of active TB was significantly lower than that of X-pert MTB/RIF (64.6% vs. 85.4%, P = 0.031). Of the 106 pathogen-negative cases, 48 were ultimately considered non-infectious diseases, with a negative predictive value of 45.3%. Of the 381 pathogen-positive cases, 311 were eventually diagnosed as CAP, with a positive predictive value of 81.6%. A total of 487 patients were included in the evaluation of the therapeutic effect, and 67.1% improved with initial empirical antibiotic treatment. Of the 163 patients in which bacteria were detected, 77.9% improved with antibacterial therapy; of the 85 patients in which fungi were detected, 12.9% achieved remission after antifungal therapy. CONCLUSIONS Overall, mNGS had unique advantages in the detection of suspected CAP pathogens. However, mNGS was not superior to X-pert MTB/RIF for the diagnosis of TB. In addition, mNGS was not necessary as a routine test for all patients admitted with suspected CAP. Furthermore, when fungi are detected by mNGS, antifungal therapy should be cautious.
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Affiliation(s)
- Mengling Liu
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haiyue Zhang
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Liangyu Li
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jieyu Mao
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ruiyun Li
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jing Yin
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaojun Wu
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
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Qian M, Li C, Zhang M, Zhan Y, Zhu B, Wang L, Shen Q, Yue L, Chen H, Cheng Y. Blood metagenomics next-generation sequencing has advantages in detecting difficult-to-cultivate pathogens, and mixed infections: results from a real-world cohort. Front Cell Infect Microbiol 2023; 13:1268281. [PMID: 38188631 PMCID: PMC10768086 DOI: 10.3389/fcimb.2023.1268281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Background Blood is a common sample source for metagenomics next-generation sequencing (mNGS) in clinical practice. In this study, we aimed to detect the diagnostic value of blood mNGS in a large real-world cohorts. Methods Blood mNGS results of 1,046 cases were collected and analyzed along with other laboratory tests. The capabilities and accuracy of blood mNGS were compared with other conventional approaches. Results Both the surgical department and the intensive care unit had a positive rate of over 80% in blood mNGS. The positive rate of mNGS was consistent with clinical manifestations. Among the 739 positive samples, 532 were detected as mixed infections. Compared to pathogen cultures, the negative predictive value of blood mNGS for bacteria and fungi detection was 98.9% [95%CI, 96.9%-100%], with an accuracy rate of 89.39%. When compared with polymer chain reaction, the consistency rates of blood mNGS for virus identification were remarkably high. Conclusions Blood mNGS have significant advantages in detecting difficult-to-cultivate bacteria or fungi, viruses, and mixed infections, which benefits patients of surgery department the most. Samples other than blood are recommended for mNGS test if a specific infection is suspected. The reporting threshold and reporting criteria of blood mNGS need to be optimized.
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Affiliation(s)
- Mengjia Qian
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chang Li
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miaomiao Zhang
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanxia Zhan
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Bijun Zhu
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingyan Wang
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qi Shen
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lei Yue
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hao Chen
- Department of Thoracic Surgery, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, China
| | - Yunfeng Cheng
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, China
- Department of Hematology, Zhongshan Hospital Qingpu Branch, Fudan University, Shanghai, China
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Li S, Tong J, Li H, Mao C, Shen W, Lei Y, Hu P. L. pneumophila Infection Diagnosed by tNGS in a Lady with Lymphadenopathy. Infect Drug Resist 2023; 16:4435-4442. [PMID: 37435234 PMCID: PMC10332418 DOI: 10.2147/idr.s417495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/27/2023] [Indexed: 07/13/2023] Open
Abstract
We report a case of a 34-year-old lady with multiple joint pain. Autoimmune diseases were considered first with a positive result of anti-Ro antibody and her right knee joint cavity effusion. Later, bilateral interstitial changes in her lungs and mediastinal lymphadenopathy were found after chest CT scanning. Empirical quinolone therapy was given although pathological examinations of blood, sputum and bronchoalveolar lavage fluid (BALF) did not find anything. Finally, Legionella pneumophila was identified by target next-generation sequencing (tNGS) detection. This case highlighted the timely use of tNGS, a new tool with fast speed, high accuracy and effective cost, could help to identify atypical infection and start an early therapy.
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Affiliation(s)
- Shiying Li
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Jin Tong
- Department of Respiratory Medicine, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Hu Li
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Chenxue Mao
- Department of Laboratory Diagnosis, ChongQing KingMed Center for Clinical Laboratory Co., Ltd, Chongqing, 400050, People’s Republic of China
| | - Wei Shen
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Yu Lei
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Peng Hu
- Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, People’s Republic of China
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Du R, Feng Y, Wang Y, Huang J, Tao Y, Mao H. Metagenomic next-generation sequencing confirms the diagnosis of Legionella pneumonia with rhabdomyolysis and acute kidney injury in a limited resource area: a case report and review. Front Public Health 2023; 11:1145733. [PMID: 37228720 PMCID: PMC10205016 DOI: 10.3389/fpubh.2023.1145733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023] Open
Abstract
Background Legionella pneumonia, rhabdomyolysis, and acute kidney injury are called the Legionella triad, which is rare and associated with a poor outcome and even death. Early diagnosis and timely treatment are essential for these patients. Case presentation A 63-year-old man with cough, fever, and fatigue was initially misdiagnosed with common bacterial infection and given beta-lactam monotherapy but failed to respond to it. Conventional methods, including the first Legionella antibody test, sputum smear, and culture of sputum, blood, and bronchoalveolar lavage fluid (BALF) were negative. He was ultimately diagnosed with a severe infection of Legionella pneumophila by metagenomics next-generation sequencing (mNGS). This patient, who had multisystem involvement and manifested with the rare triad of Legionella pneumonia, rhabdomyolysis, and acute kidney injury, finally improved after combined treatment with moxifloxacin, continuous renal replacement therapy, and liver protection therapy. Conclusion Our results showed the necessity of early diagnosis of pathogens in severe patients, especially in Legionnaires' disease, who manifested with the triad of Legionella pneumonia, rhabdomyolysis, and acute kidney injury. mNGS may be a useful tool for Legionnaires' disease in limited resource areas where urine antigen tests are not available.
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Affiliation(s)
- Rao Du
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yinhe Feng
- Department of Respiratory and Critical Care Medicine, Deyang People's Hospital, Affiliated Hospital of Chengdu College of Medicine, Deyang, China
| | - Yubin Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jifeng Huang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yuhan Tao
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hui Mao
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
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Huang PH, Huang YT, Lee PH, Tseng CH, Liu PY, Liu CW. Diagnosis of Legionnaires' Disease Assisted by Next-Generation Sequencing in a Patient with COVID-19. Infect Drug Resist 2023; 16:355-362. [PMID: 36714349 PMCID: PMC9880021 DOI: 10.2147/idr.s396254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Coinfection in COVID-19 patients is associated with worsening outcome. Among patients with COVID-19, Legionella pneumophila, a common cause of pneumonia, has been reported as a co-occurring respiratory infection. A nonspecific clinical presentation, however, makes an early diagnosis difficult. Bronchoalveolar lavage fluid was collected from a patient suffering from COVID-19 and presenting with pneumonia and sent for metagenomic analysis. Differential abundance analysis was carried out by comparing each taxon reads per million between the bronchoalveolar lavage fluid sample and the negative control. Two replicates of metagenomic sequencing were conducted on bronchoalveolar lavage fluid samples. Within each replicated sequencing, one negative control was sequenced for comparison of taxon abundance in the BALF sample. In both replicates, Legionella pneumophila was the only taxon with significantly higher abundance when compared with the negative control. PCR of the bronchoalveolar further confirmed the presence of L. pneumophila. Several studies have estimated that the incidence of Legionnaires' disease co-infection in patients with COVID-19 infection is approximately 0% to 1.5%. There are some common characteristics of COVID-19 and co-infection with Legionnaires' disease, making it difficult to diagnose bacterial infection early. The diagnosis of these cases is important due to the different treatments used. Current diagnostic tests for Legionnaires' disease include conventional culture, urinary antigen for L. pneumophila serogroup 1, polymerase chain reaction, direct fluorescent antibody stain, and paired serology. The current study demonstrated that metagenomics is a promising approach that facilitated the diagnosis of Legionnaires' disease.
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Affiliation(s)
- Po-Hsiu Huang
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Po-Hsin Lee
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan,Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chien-Hao Tseng
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Po-Yu Liu
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Correspondence: Po-Yu Liu; Chia-Wei Liu, Tel +886 4 2359 2525, Fax +886 4 2359 2525 2111, Email ;
| | - Chia-Wei Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
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Chen H, Liang Y, Wang R, Wu Y, Zhang X, Huang H, Yu X, Hong M, Yang J, Liao K, Xu H, Liu M, Chen P, Chen Y. Metagenomic next-generation sequencing for the diagnosis of Pneumocystis jirovecii Pneumonia in critically pediatric patients. Ann Clin Microbiol Antimicrob 2023; 22:6. [PMID: 36647095 PMCID: PMC9841943 DOI: 10.1186/s12941-023-00555-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
OBJECTIVE The aim of this study was to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) for the diagnosis of Pneumocystis jirovecii Pneumonia (PCP) in critically pediatric patients. METHODS Seventeen critically pediatric patients with PCP and sixty patients diagnosed with non-PCP pneumonia who were admitted in pediatric intensive care unit between June 2018 and July 2021 were enrolled. Conventional methods and mNGS for detecting Pneumocystis jirovecii (P. jirovecii) were compared. The patients' demographics, comorbidities, laboratory test results, antibiotic treatment response and 30 day mortality were analyzed. RESULT The mNGS showed a satisfying diagnostic performance with a sensitivity of 100% in detecting P. jirovecii compared with Gomori methenamine silver staining (5.9%), serum (1,3)-β-D-glucan (86.7%) and and LDH (55.6%). The diagnostic specificity of mNGS for PCP was higher than that of serum BDG (56.7%) and LDH (71.4%). In PCP group, over one thirds' cases had mixed infections. Compared with survivors, non-survivors had higher stringently mapped read numbers (SMRNs) in bronchoalveolar lavage fluid (BALF) sample (P < 0.05), suggesting SMRNs were closely associated with the severity of response. The detection for P. jirovecii by mNGS both in BALF and blood samples reached a concordance rate of 100%, and the SMRNs in the BALF were remarkably higher than that in blood samples. Initial antimicrobial treatment was modified in 88.2% of PCP patients based on the mNGS results. CONCLUSION The mNGS is a potential and efficient technology in diagnosing PCP and shows a satisfying performance in the detection of co-pathogens. Both blood and BALF samples for mNGS are suggested for the presumptive diagnosis of PCP.
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Affiliation(s)
- Hengxin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Yujian Liang
- Department of Pediatric Intensive Care Unit, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Ruizhi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Yijie Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China
| | - Xiaoyun Zhang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China
| | - Hao Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Xuegao Yu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Mengzhi Hong
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Juhua Yang
- Vision Medicals Co., Ltd, Guangzhou, China
| | - Kang Liao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Hongxu Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Min Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
| | - Yili Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
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Zhao X, Bai LP, Li BY, Yue ZZ, Zhao YC, Zhao XY. Comparison of mNGS and conventional culture in non-organ transplant critically ill patients supported by ECMO: a single-center study. Front Cell Infect Microbiol 2023; 13:1146088. [PMID: 37139490 PMCID: PMC10149872 DOI: 10.3389/fcimb.2023.1146088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/28/2023] [Indexed: 05/05/2023] Open
Abstract
Objectives Infection is one of the important causes of death in intensive care unit (ICU) patients. At present, there are few articles focused on the detailed analysis of pathogenic microorganisms detected in different therapy periods of critically ill patients supported by extracorporeal membrane oxygenation (ECMO). Methods From October 2020 to October 2022, ECMO-assisted patients who underwent multiple times of both metagenomic next-generation sequencing (mNGS) test and conventional culture were enrolled continuously in the First Affiliated Hospital of Zhengzhou University. The baseline data, laboratory test results, and pathogenic microorganisms detected by mNGS and traditional culture in different time periods were recorded and analyzed. Results In the present study, 62 patients were included finally. According to whether the patients survived at discharge, they were divided into the survivor group (n = 24) and the non-survivor group (n = 38). Then, according to the different types of ECMO support, they were divided into the veno-venous ECMO (VV ECMO) group (n = 43) and the veno-arterial ECMO (VA ECMO) group (n = 19). The summit period of specimens of traditional culture and mNGS detection of ECMO patients was 7 days after admission, and the largest number of specimens of surviving patients appeared after ECMO withdrawal. The total number of traditional culture specimens was 1,249, the positive rate was 30.4% (380/1,249), and the positive rate of mNGS was 79.6% (82/103). A total of 28 kinds of pathogenic microorganisms were cultured from conventional culture, and 58 kinds of pathogenic microorganisms were detected by mNGS, including Mycobacterium, Rickettsia, and Chlamydia psittaci. In conventional culture, the most frequent Gram-negative bacteria, Gram-positive bacteria, and fungi were Klebsiella pneumoniae, Corynebacterium striatum, and Candida glabrata, and those with the highest frequency of occurrence in mNGS detection were Acinetobacter baumannii, Enterococcus faecium, and Aspergillus flavus. Conclusions Throughout the whole treatment process, different kinds of suspicious biological specimens of high-infection-risk ICU patients supported by ECMO should undergo both mNGS detection and traditional culture early and repeatedly.
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Affiliation(s)
- Xi Zhao
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lin-Peng Bai
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Bo-Yan Li
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhen-Zhen Yue
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yang-Chao Zhao
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Yang-Chao Zhao, ; Xiao-Yan Zhao,
| | - Xiao-Yan Zhao
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Yang-Chao Zhao, ; Xiao-Yan Zhao,
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Xu Y, Wang Y, Wu J, Zhao X, Huang G, Fang J. Coinfection with Hypervirulent Klebsiella pneumoniae and Aspergillus flavus in a Critically Ill Patient with Aspergillus Overlap Syndrome: A Case Report. Infect Drug Resist 2022; 15:7823-7830. [PMID: 36600954 PMCID: PMC9807123 DOI: 10.2147/idr.s394004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/17/2022] [Indexed: 12/30/2022] Open
Abstract
Pulmonary aspergillosis is generally categorized into three groups: allergic bronchopulmonary aspergillosis, chronic pulmonary aspergillosis and invasive pulmonary aspergillosis. Aspergillus overlap syndromes (AOS) defined as the occurrence of more than one form of aspergillus disease in a single individual is not common. We present a 62-year-old-male patient with tachypnea, hypoxemia and shock after 4 weeks of cough, expectoration and intermittent hemoptysis, and 2 days of hyperpyrexia. Cardiac arrest occurring during tracheal intubation was resuscitated successfully. Laboratory examination showed acute kidney failure and severe myelosuppression with leukopenia and thrombocytopenia. Chest computed tomography (CT) scan showed the cavity with aspergilloma in the right upper lung lobe, a mass of consolidation in the right lower lung lobe and hyperdense shadow bronchiectasis in the left lower lobe. Bronchoscopy showed lots of sputum occluding the opening of the right airway bronchus. Laboratory examination showed significantly increased C-reactive protein (CRP) and procalcitonin concentration, serum (1,3)-β-D-glucan (BDG) and aspergillus immunoglobulin G (IgG) levels were also elevated. The metagenomic next-generation sequencing and sputum cultures revealed Klebsiella pneumoniae and Aspergillus flavus infection. Pulmonary aspergillosis, invasive aspergillosis infection and severe pneumonia were diagnosed. Initial caspofungin and meropenem followed by piperacillin-tazobactam sodium and voriconazole were administrated in combination. Continuous renal replacement therapy and mechanical ventilation were also performed. The patient's condition gradually recovered. Oral antifungal therapy was continued for 1 year after discharge and CT images gradually improved. Coinfections with K. pneumoniae and A. flavus in a patient with AOS will complicate clinical conditions. A search of PubMed showed few reports of similar cases. Clinicians should pay enough attention to the polymicrobial interactions and improve clinical management strategies, especially in critically ill patient with AOS.
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Affiliation(s)
- Yuansheng Xu
- Department of Emergency, Affiliated Hangzhou First People`s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yi Wang
- Department of Emergency, Affiliated Hangzhou First People`s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Jinhong Wu
- Department of Emergency, Affiliated Hangzhou First People`s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Xue Zhao
- Department of Emergency, Affiliated Hangzhou First People`s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Ganying Huang
- Department of Emergency, Affiliated Hangzhou First People`s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Jinyan Fang
- Department of Emergency, Affiliated Hangzhou First People`s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China,Correspondence: Jinyan Fang, Department of Emergency, Affiliated Hangzhou First People`s Hospital, Zhejiang University School of Medicine, No. 261 Huansha Road, Hangzhou, Zhejiang Province, 310006, People’s Republic of China, Email
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10
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Niu S, Zhao L. Metagenomic next-generation sequencing clinches the diagnosis of Legionella pneumonia in a patient with acute myeloid leukemia: A case report and literature review. Front Cell Infect Microbiol 2022; 12:924597. [PMID: 36478673 PMCID: PMC9720252 DOI: 10.3389/fcimb.2022.924597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/06/2022] [Indexed: 11/22/2022] Open
Abstract
Legionella pneumonia caused by Legionella pneumophila is a multi-system disease that is a life-threatening, acute, and severe form of pneumonia. L. pneumophila is widespread and the clinical manifestations of Legionella pneumonia are similar to those of typical and atypical pneumonia. Current diagnostic scores and radiologic evidence have limited diagnostic value. Thus, it is likely that many cases of Legionella pneumonia remain unreported. We describe a woman with a medical history of acute myeloid leukemia who suffered from repeated fever, and no relief following initial empirical antibiotic treatment. Ultimately, she was diagnosed with Legionella pneumonia based on metagenomic next-generation sequencing (mNGS). We also performed a systematic review of the literature and identified 5 other patients who were diagnosed with Legionella pneumonia using mNGS, and reviewed their clinical characteristics, biological characteristics, epidemiological features, laboratory results, clinical findings, and treatments. This literature review showed that accurate etiological diagnosis is becoming increasingly essential for a definitive diagnosis and treatment strategies. The clinical manifestations of Legionella pneumonia are non-specific, and many routine laboratory diagnostic tests cannot identify Legionella. mNGS, an indispensable approach for identifying microorganisms, can provide a promising tool for the rapid and accurate etiological diagnosis methods contributing to early diagnosis, early treatment, and improved prognosis, especially for uncommon species such as L. pneumophila.
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Affiliation(s)
- Siqiang Niu
- Zhengzhou University, Zhengzhou, Henan, China,Henan Provincial People’s Hospital, Zhengzhou, Henan, China,Xinxiang City Central Hospital, Xinxiang, Henan, China
| | - Limin Zhao
- Department of Respiratory and Critical Care Medicine, Henan Provincial People’s Hospital, Zhengzhou, Henan, China,People's Hospital of Zhengzhou University, Zhengzhou, Henan, China,People's Hospital of Henan University, Zhengzhou, Henan, China,*Correspondence: Limin Zhao,
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11
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Zhao M, Yue R, Wu X, Gao Z, He M, Pan L. The diagnostic value of metagenomic next-generation sequencing for identifying Pneumocystis jirovecii infection in non-HIV immunocompromised patients. Front Cell Infect Microbiol 2022; 12:1026739. [PMID: 36389151 PMCID: PMC9647189 DOI: 10.3389/fcimb.2022.1026739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background Pneumocystis jirovecii pneumonia (PJP) remains an important cause of morbidity and mortality in non-HIV immunocompromised patients especially in transplant recipients. But its diagnosis remains challenging due to the insuffificient performance of conventional methods for diagnosing Pneumocystis jirovecii(P. jirovecii) infection. Therefore, the auxiliary diagnostic function of metagenomics next-generation sequencing (mNGS) in clinical practice is worth of exploring. Method 34 non-HIV immunocompromised patients who were diagnosed as PJP by clinical manifestations, imaging findings, immune status of the host, and Methenamine silver staining were tested by mNGS from October 2018 to December 2020 in Sichuan Provincial People’s Hospital. The clinical performances of mNGS for P. jirovecii infection diagnosis were also evaluated with genome reads abundance and comparing with other traditional diagnostic methods. Results We diagnosed a total of 34 non-HIV PJP patients by the clinical composite diagnosis. Our data shows that, compared with the clinical microbiological test, the detection rate of mNGS for P. jirovecii in non-HIV infected PJP patients is significantly higher than that of Methenamine silver staining and serum 1-3-β-D-glucan. mNGS can be used as an auxiliary diagnostic tool to help diagnosis. The number of reads mapped to the genome of P. jirovecii and the duration of patients from onset to sampling collection were statistically significant between the two groups (Reads>100 and Reads ≤ 100) (8days vs. 23days, p=0.020). In addition, univariate analysis showed that C-reactive protein (15.8mg/L vs.79.56mg/L, p=0.016), lactate dehydrogenase (696U/l vs. 494U/l, p=0.030) and procalcitonin (0.09ng/ml vs. 0.59ng/ml, p=0.028) was also statistically significant between the two groups. Conclusions An effective detection rate was achieved in PJP patients using mNGS testing of bronchoalveolar lavage fluid (BALF) or blood. The study also confirmed that the abundance of reads of P. jirovecii is related to the interval between the onset and sample collection. And the inflammation status during simultaneous mNGS detection might determine the abundance of pathogens. Hence, we conclude that the mNGS strategy could benefit disease diagnosis as well as treatment when complicated clinical infections appeared.
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Affiliation(s)
- Mengyi Zhao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Ruiming Yue
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Xiaoxiao Wu
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Zhan Gao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
- *Correspondence: Miao He, ; Lingai Pan,
| | - Lingai Pan
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- *Correspondence: Miao He, ; Lingai Pan,
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12
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Iliadi V, Staykova J, Iliadis S, Konstantinidou I, Sivykh P, Romanidou G, Vardikov DF, Cassimos D, Konstantinidis TG. Legionella pneumophila: The Journey from the Environment to the Blood. J Clin Med 2022; 11:jcm11206126. [PMID: 36294446 PMCID: PMC9605555 DOI: 10.3390/jcm11206126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/26/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
An outbreak of a potentially fatal form of pneumonia in 1976 and in the annual convention of the American Legion was the first time that Legionella spp. was identified. Thereafter, the term Legionnaires’ disease (LD) was established. The infection in humans is transmitted by the inhalation of aerosols that contain the microorganisms that belong to the Legionellaceae family and the genus Legionella. The genus Legionella contains genetically heterogeneous species and serogroups. The Legionella pneumophila serogroup 1 (Lp1) is the most often detected strain in outbreaks of LD. The pathogenesis of LD infection initiates with the attachment of the bacterial cells to the host cells, and subsequent intracellular replication. Following invasion, Legionella spp. activates its virulence mechanisms: generation of specific compartments of Legionella-containing vacuole (LCV), and expression of genes that encode a type IV secretion system (T4SS) for the translocation of proteins. The ability of L. pneumophila to transmigrate across the lung’s epithelium barrier leads to bacteremia, spread, and invasion of many organs with subsequent manifestations, complications, and septic shock. The clinical manifestations of LD depend on the bacterial load in the aerosol, the virulence factors, and the immune status of the patient. The infection has two distinct forms: the non- pneumatic form or Pontiac fever, which is a milder febrile flu-like illness, and LD, a more severe form, which includes pneumonia. In addition, the extrapulmonary involvement of LD can include heart, brain, abdomen, and joints.
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Affiliation(s)
- Valeria Iliadi
- Izhevsk State Medical Academy, Kommunarov Street 281, 426034 Izhevsk, Russia
| | - Jeni Staykova
- Faculty of Public Health, Medical University of Sofia, Byalo More Str. 8, 1527 Sofia, Bulgaria
| | - Sergios Iliadis
- Izhevsk State Medical Academy, Kommunarov Street 281, 426034 Izhevsk, Russia
| | | | - Polina Sivykh
- State Budgetary Health City Polyclinic No 2 (GBUZ GB2) of Krasnodar, Seleznev Street 4/10, 350059 Krasnodar, Russia
| | - Gioulia Romanidou
- Nephrology Department, General Hospital “Sismanogleio”, 69100 Komotini, Greece
| | - Daniil F. Vardikov
- Russian Research Center for Radiology and Surgical Technologies of the Ministry of Health of the Russian Federation, Tkachey Str. 70-16, 192029 St. Petersburg, Russia
| | - Dimitrios Cassimos
- Pediatric Department, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Theocharis G. Konstantinidis
- Blood Transfusion Center, University General Hospital of Alexandroupolis Dragana Campus, 68100 Alexandroupolis, Greece
- Correspondence: ; Tel.: +30-2551-352005
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13
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Hou JN, Liu HD, Tan QY, Cao FA, Wang SL, Yao MY, Zhao YC. Risk factors of in-hospital mortality in patients with pneumocystis pneumonia diagnosed by metagenomics next-generation sequencing. Front Cell Infect Microbiol 2022; 12:994175. [PMID: 36225233 PMCID: PMC9549864 DOI: 10.3389/fcimb.2022.994175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives The metagenomic next-generation sequencing (mNGS) test is useful for rapid and accurate detection and identification of pathogenic microorganisms. The aim of the present study was to investigate the factors associated with in-hospital mortality in pneumocystis pneumonia (PCP) patients with mNGS-assisted diagnosis. Methods Our study enrolled 154 patients with mNGS-positive PCP from August 2018 to February 2022 at the First Affiliated Hospital of Zhengzhou University respectively. Patients were divided into the survivor group (n=98) and the death group (n=56) according to whether in-hospital death occurred. Baseline characteristics, patients’ pre-hospital symptoms and patients’ CT imaging performance during hospitalization were carefully compared between the two groups. Risk factors for the occurrence of in-hospital death were sought by selecting indicators that were significantly different between the two groups for modelling and performing multiple logistic regression analysis. Results Compared with the in-hospital death patients, the survivors were younger and had higher levels of albumin (ALB) (age: 50.29 ± 14.63 years vs 59.39 ± 12.27 years, p<0.001; ALB: 32.24 ± 5.62 g/L vs 29.34 ± 5.42g/L, p=0.002; respectively), while the levels of lactate dehydrogenase (LDH) and C-reactive protein CRP were lower (LDH: 574.67 ± 421.24 U/L vs 960.80 ± 714.94 U/L, p=0.001; CRP: 54.97 ± 55.92 mg/L vs80.45 ± 73.26 mg/L, p=0.018; respectively). Multiple logistic regression analysis revealed that age, the baseline LDH and CRP levels were all positively associated with high in-hospital mortality [age: OR(95%CI): 1.115 (1.062-1.172), p<0.001; LDH: OR(95%CI): 1.002 (1.001-1.003), p<0.001; CRP: OR(95%CI): 1.008 (1.000-1.017), p=0.045; respectively] while the platelet counts was negatively associated with it [OR(95%CI): 0.986 (0.979-0.992), p<0.001]. Conclusions Old age, high baseline levels of LDH and CRP and low platelet counts were risk factors of the in-hospital mortality in mNGS positive PCP patients.
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Affiliation(s)
- Jun-Na Hou
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Heng-Dao Liu
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiu-Yue Tan
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng-An Cao
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shi-Lei Wang
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Meng-Ying Yao
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Meng-Ying Yao, ; Yang-Chao Zhao,
| | - Yang-Chao Zhao
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Meng-Ying Yao, ; Yang-Chao Zhao,
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14
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Zhao YC, Ding YZ, Zhao X, Fu GW, Huang MJ, Li XX, Sun QQ, Kan YB, Li J, Wang SL, Ma WT, Xu QF, Liu QL, Li HB. Role and Clinical Application of Metagenomic Next-Generation Sequencing in Immunocompromised Patients With Acute Respiratory Failure During Veno-Venous Extracorporeal Membrane Oxygenation. Front Cell Infect Microbiol 2022; 12:877205. [PMID: 36034706 PMCID: PMC9414489 DOI: 10.3389/fcimb.2022.877205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022] Open
Abstract
Objectives There are few studies of metagenomic next-generation sequencing (mNGS) in immunocompromised patients assisted by veno-venous extracorporeal membrane oxygenation (vv-ECMO). The present study is aimed to investigate the pathogen-detected effect and clinical therapy value of mNGS technologies in immunocompromised patients assisted by vv-ECMO. Methods Our study retrospectively enrolled 46 immunocompromised patients supported by vv-ECMO from Jan 2017 to June 2021 at the First Affiliated Hospital of Zhengzhou University, respectively. Patients were divided into the deterioration group (Group D) (n = 31) and improvement group (Group I) (n = 15) according to their outcomes. Baseline characteristics and etiological data of patients during hospitalization of 2 groups were compared. The pathogens detected by mNGS and antibiotic regimens guided by mNGS in immunocompromised patients assisted by vv-ECMO were analyzed. Results Compared with Group I, the deterioration patients showed a higher percentage of chronic obstructive pulmonary disease (COPD) (32.3% vs. 6.7%, p < 0.01) and were significantly older (47.77 ± 16.72 years vs. 32 ± 15.05 years, p < 0.01). Within 48 h of being ECMO assisted, the consistency of the samples detected by traditional culture and mNGS at the same time was good (traditional culture vs. mNGS detection, the positive rate of bronchoalveolar lavage fluid (BALF) culture: 26.1% vs. 30.4%; the positive rate of blood sample culture: 12.2% vs. 12.2%, p > 0.05). However, mNGS detected far more pathogen species and strains than conventional culture (30 strains vs. 78 strains, p < 0.01); the most popular pathogen was Klebsiella pneumoniae. Parts of patients had their antibiotic treatment adjustments, and the improvement patients showed less usage of broad-spectrum antibiotics. Conclusions mNGS may play a relatively important role in detecting mixed pathogens and personalized antibiotic treatment in immunocompromised patients assisted by vv-ECMO.
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Affiliation(s)
- Yang-Chao Zhao
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Yang-Chao Zhao,
| | - Yan-Zhong Ding
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xi Zhao
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guo-Wei Fu
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ming-Jun Huang
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xing-Xing Li
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qian-Qian Sun
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ya-Bai Kan
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Li
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shi-Lei Wang
- Department of Respiration, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wen-Tao Ma
- Department of Respiration, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qin-Fu Xu
- Department of Respiration, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qi-Long Liu
- Department of Surgery ICU, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hong-Bin Li
- Department of Surgery ICU, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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15
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Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: a Multicenter Retrospective Study. Microbiol Spectr 2022; 10:e0247321. [PMID: 35943274 PMCID: PMC9431624 DOI: 10.1128/spectrum.02473-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has been gradually applied to clinical practice due to its unbiased characteristics of pathogen detection. However, its diagnostic performance and clinical value in suspected pulmonary infection need to be evaluated. We systematically reviewed the clinical data of 246 patients with suspected pulmonary infection from 4 medical institutions between January 2019 and September 2021. The diagnostic performances of mNGS and conventional testing (CT) were systematically analyzed based on bronchoalveolar lavage fluid (BALF). The impacts of mNGS and CT on diagnosis modification and treatment adjustment were also assessed. The positive rates of mNGS and CT were 47.97% and 23.17%, respectively. The sensitivity of mNGS was significantly higher than that of CT (53.49% versus 23.26%, P < 0.01), especially for infections of Mycobacterium tuberculosis (67.86% versus 17.86%, P < 0.01), atypical pathogens (100.00% versus 7.14%, P < 0.01), viruses (92.31% versus 7.69%, P < 0.01), and fungi (78.57% versus 39.29%, P < 0.01). The specificity of mNGS was superior to that of CT, with no statistical difference (90.32% versus 77.42%, P = 0.167). The positive predictive value (PPV) and negative predictive value (NPV) of mNGS were 97.46% and 21.88%, respectively. Diagnosis modification and treatment adjustment were conducted in 32 (32/246, 13.01%) and 23 (23/246, 9.35%) cases, respectively, according to mNGS results only. mNGS significantly improved the diagnosis of suspected pulmonary infection, especially infections of M.tuberculosis, atypical pathogens, viruses, and fungi, and it demonstrated the pathogen distribution of pulmonary infections. It is expected to be a promising microbiological detection and diagnostic method in clinical practice. IMPORTANCE Pulmonary infection is a heterogeneous and complex infectious disease with high morbidity and mortality worldwide. In clinical practice, a considerable proportion of the etiology of pulmonary infection is unclear, microbiological diagnosis being challenging. Metagenomic next-generation sequencing detects all nucleic acids in a sample in an unbiased manner, revealing the microbial community environment and organisms and improving the microbiological detection and diagnosis of infectious diseases in clinical settings. This study is the first multicenter, large-scale retrospective study based entirely on BALF for pathogen detection by mNGS, and it demonstrated the superior performance of mNGS for microbiological detection and diagnosis of suspected pulmonary infection, especially in infections of Mycobacterium tuberculosis, atypical pathogens, viruses, and fungi. It also demonstrated the pathogen distribution of pulmonary infections in the real world, guiding targeted treatment and improving clinical management and prognoses.
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Legionnaires' Disease: Update on Diagnosis and Treatment. Infect Dis Ther 2022; 11:973-986. [PMID: 35505000 PMCID: PMC9124264 DOI: 10.1007/s40121-022-00635-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
Abstract
Legionellosis is the infection caused by bacteria of the genus Legionella, including a non-pneumonic influenza-like syndrome, and Legionnaires’ disease is a more serious illness characterized by pneumonia. Legionellosis is becoming increasingly important as a public health problem throughout the world; although it is an underreported disease, studies have consistently documented a high incidence. In addition, health costs associated with the disease are high. Diagnosis of Legionnaires’ disease is based mainly on the detection of Legionella pneumophila serogroup 1 antigen in urine. However, there have been advances in detection tests for patients with legionellosis. New methodologies show greater sensitivity and specificity, detect more species and serogroups of Legionella spp., and have the potential for use in epidemiological studies. Testing for Legionella spp. is recommended at hospital admission for severe community-acquired pneumonia, and antibiotics directed against Legionella spp. should be included early as empirical therapy. Inadequate or delayed antibiotic treatment in Legionella pneumonia has been associated with a worse prognosis. Either a fluoroquinolone (levofloxacin or moxifloxacin) or a macrolide (azithromycin preferred) is the recommended first-line therapy for Legionnaires’ disease; however, little information is available regarding adverse events or complications, or about the duration of antibiotic therapy and its association with clinical outcomes. Most published studies evaluating antibiotic treatment for Legionnaires’ disease are observational and consequently susceptible to bias and confounding. Well-designed studies are needed to assess the usefulness of diagnostic tests regarding clinical outcomes, as well as randomized trials comparing fluoroquinolones and macrolides or combination therapy that evaluate outcomes and adverse events.
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17
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Rodriguez KM, Ramchandar N, Coufal NG. Plasma cell free next-generation sequencing detects an unusual pneumonia pathogen in an immunocompetent adolescent with acute respiratory distress syndrome. Front Pediatr 2022; 10:1034632. [PMID: 36545658 PMCID: PMC9760936 DOI: 10.3389/fped.2022.1034632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
This case details a rapid diagnosis of legionella pneumonia causing severe acute respiratory distress syndrome (ARDS) in an otherwise healthy adolescent through plasma microbial cell-free DNA next generation sequencing (mcfDNA-NGS). Diagnosis by mcfDNA-NGS of this unexpected pathogen led to narrowing of antimicrobials and the addition of glucocorticoids as adjunctive therapy for ARDS.
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Affiliation(s)
- Katherine M Rodriguez
- Division of Pediatric Critical Care, Department of Pediatrics, University of California, San Diego, CA, United States.,Division of Pediatric Critical Care, Department of Pediatrics, Rady Children's Hospital San Diego, San Diego, CA, United States
| | - Nanda Ramchandar
- Division of Infectious Disease, Department of Pediatrics, Navy Medical Center, San Diego, CA, United States.,Division of Infectious Disease, Department of Pediatrics San Diego, Rady Children's Hospital San Diego, San Diego, CA, United States
| | - Nicole G Coufal
- Division of Pediatric Critical Care, Department of Pediatrics, University of California, San Diego, CA, United States.,Division of Pediatric Critical Care, Department of Pediatrics, Rady Children's Hospital San Diego, San Diego, CA, United States
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