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Huang Z, Hu B, Li J, Feng M, Wang Z, Huang F, Xu H, Liu L, Shang W. Metagenomic versus targeted next-generation sequencing for detection of microorganisms in bronchoalveolar lavage fluid among renal transplantation recipients. Front Immunol 2024; 15:1443057. [PMID: 39253087 PMCID: PMC11381253 DOI: 10.3389/fimmu.2024.1443057] [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: 06/03/2024] [Accepted: 08/01/2024] [Indexed: 09/11/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS), which provides untargeted and unbiased pathogens detection, has been extensively applied to improve diagnosis of pulmonary infection. This study aimed to compare the clinical performance between mNGS and targeted NGS (tNGS) for microbial detection and identification in bronchoalveolar lavage fluid (BALF) from kidney transplantation recipients (KTRs). Methods BALF samples with microbiological results from mNGS and conventional microbiological test (CMT) were included. For tNGS, samples were extracted, amplified by polymerase chain reaction with pathogen-specific primers, and sequenced on an Illumina Nextseq. Results A total of 99 BALF from 99 KTRs, among which 93 were diagnosed as pulmonary infection, were analyzed. Compared with CMT, both mNGS and tNGS showed higher positive rate and sensitivity (p<0.001) for overall, bacterial and fungal detection. Although the positive rate for mNGS and tNGS was comparable, mNGS significantly outperformed tNGS in sensitivity (100% vs. 93.55%, p<0.05), particularly for bacteria and virus (p<0.001). Moreover, the true positive rate for detected microbes of mNGS was superior over that of tNGS (73.97% vs. 63.15%, p<0.05), and the difference was also significant when specific for bacteria (94.59% vs. 64.81%, p<0.001) and fungi (93.85% vs. 72.58%, p<0.01). Additionally, we found that, unlike most microbes such as SARS-CoV-2, Aspergillus, and EBV, which were predominantly detected from recipients who underwent surgery over 3 years, Torque teno virus (TTV) were principally detected from recipients within 1-year post-transplant, and as post-transplantation time increased, the percentage of TTV positivity declined. Conclusion Although tNGS was inferior to mNGS owing to lower sensitivity and true positive rate in identifying respiratory pathogens among KTRs, both considerably outperformed CMT.
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Affiliation(s)
- Zhaoru Huang
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bingxue Hu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, China
| | - Jinfeng Li
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Min Feng
- Surgical Intensive Care Unit, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Wang
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fengxiang Huang
- Respiratory Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huan Xu
- Center for Infectious Diseases, Vision Medicals Co., Ltd, Guangzhou, China
| | - Lei Liu
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenjun Shang
- Kidney Transplantation Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Zeng W, Liang Y, He X, Chen F, Xiong J, Wen Z, Tang L, Chen X, Zhang J. Exploring the pathogen diagnosis and prognostic factors of severe COVID-19 using metagenomic next-generation sequencing: A retrospective study. J Med Biochem 2024; 43:528-536. [PMID: 39139158 PMCID: PMC11318844 DOI: 10.5937/jomb0-49102] [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: 01/17/2024] [Accepted: 03/21/2024] [Indexed: 08/15/2024] Open
Abstract
Background This study aimed to identify pathogens and factors that predict the outcome of severe COVID-19 by utilizing metagenomic next-generation sequencing (mNGS) technology. Methods We retrospectively analyzed data from 56 severe COVID-19 patients admitted to our hospital between December 2022 and March 2023. We analyzed the pathogen types and strains detected through mNGS and conventional microbiological testing and collected general patient information. Results In this study, 42 pathogens were detected using mNGS and conventional microbiological testing. mNGS had a significantly higher detection rate of 90.48% compared to 71.43% for conventional testing (P=0.026). A total of 196 strains were detected using both methods, with a significantly higher detection rate of 70.92% for mNGS compared to 49.49% for conventional testing (P=0.000). The 56 patients were divided into a survival group (33 cases) and a death group (23 cases) based on clinical outcomes. The survival group had significantly lower age, number of pathogens detected by mNGS, number of pathogens detected by conventional testing, APACHE-II score, SOFA score, high-sensitivity troponin, creatine kinase-MB subtype, and lactate dehydrogenase compared to the death group (P<0.05). Multivariate logistic regression analysis showed that these factors were risk factors for mortality in severe COVID-19 patients (P<0.05). In contrast, ROC curve analysis revealed that these factors had diagnostic values for mortality, with AUC values ranging from 0.657 to 0.963. The combined diagnosis of these indicators had an AUC of 0.924. Conclusions The use of mNGS technology can significantly enhance the detection of pathogens in severe cases of COVID-19 and also has a solid ability to predict clinical outcomes.
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Affiliation(s)
- Weizhong Zeng
- Zhuzhou Central Hospital, Department of Intensive Care Unit, Zhuzhou, China
| | - Yanchao Liang
- Zhuzhou Central Hospital, Department of Respiratory and Critical Care Medicine, Zhuzhou, China
| | - Xiaoyuan He
- Zhuzhou Central Hospital, Nursing Department, Zhuzhou, China
| | - Fangwei Chen
- Zhuzhou Central Hospital, Department of Respiratory and Critical Care Medicine, Zhuzhou, China
| | - Jiali Xiong
- Zhuzhou Central Hospital, Department of Respiratory and Critical Care Medicine, Zhuzhou, China
| | - Zhenhua Wen
- Zhuzhou Central Hospital, Department of Rheumatology and Immunology, Zhuzhou, China
| | - Liang Tang
- Zhuzhou Central Hospital, Department of General Internal Medicine, Zhuzhou, China
| | - Xun Chen
- Zhuzhou Central Hospital, Department of Hepatobiliary and Pancreatic Surgery, Zhuzhou, China
| | - Juan Zhang
- Zhuzhou Central Hospital, Reproductive center, Zhuzhou, China
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Ibrahim A, Chattaraj A, Iqbal Q, Anjum A, Rehman MEU, Aijaz Z, Nasir F, Ansar S, Zangeneh TT, Iftikhar A. Pneumocystis jiroveci
Pneumonia: A Review of Management in Human Immunodeficiency Virus (HIV) and Non-HIV Immunocompromised Patients. Avicenna J Med 2023; 13:23-34. [PMID: 36969352 PMCID: PMC10038753 DOI: 10.1055/s-0043-1764375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023] Open
Abstract
Pneumocystis jirovecii
pneumonia is an opportunistic fungal infection that was mainly associated with pneumonia in patients with advanced human immunodeficiency virus (HIV) disease. There has been a decline in
Pneumocystis jirovecii
pneumonia incidence in HIV since the introduction of antiretroviral medications. However, its incidence is increasing in non-HIV immunocompromised patients including those with solid organ transplantation, hematopoietic stem cell transplantation, solid organ tumors, autoimmune deficiencies, and primary immunodeficiency disorders. We aim to review and summarize the etiology, epidemiology, clinical presentation, diagnosis, and management of
Pneumocystis jirovecii
pneumonia in HIV, and non-HIV patients. HIV patients usually have mild-to-severe symptoms, while non-HIV patients present with a rapidly progressing disease. Induced sputum or bronchoalveolar lavage fluid can be used to make a definitive diagnosis of
Pneumocystis jirovecii
pneumonia. Trimethoprim-sulfamethoxazole is considered to be the first-line drug for treatment and has proven to be highly effective for
Pneumocystis jirovecii
pneumonia prophylaxis in both HIV and non-HIV patients. Pentamidine, atovaquone, clindamycin, and primaquine are used as second-line agents. While several diagnostic tests, treatments, and prophylactic regimes are available at our disposal, there is need for more research to prevent and manage this disease more effectively.
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Affiliation(s)
- Atif Ibrahim
- North Mississippi Medical Center, Tupelo, Mississippi, United States
| | - Asmi Chattaraj
- University of Pittsburgh Medical Center, McKeesport, Pennsylvania, United States
| | - Qamar Iqbal
- TidalHealth, Salisbury, Maryland, United States
| | - Ali Anjum
- King Edward Medical University, Lahore, Pakistan
| | | | | | | | - Sadia Ansar
- Rawal Institute of Health Sciences, Islamabad, Pakistan
| | - Tirdad T. Zangeneh
- Division of Infectious Diseases, Department of Medicine, University of Arizona, Tucson, Arizona, United States
| | - Ahmad Iftikhar
- Department of Internal Medicine, University of Arizona, Tucson, Arizona, United States
- Address for correspondence Ahmad Iftikhar, MD Department of Medicine, University of Arizona1525N. Campbell Avenue, PO Box 245212, Tucson, AZ 85724
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Zou J, Wang T, Qiu T, Zhou J, Chen Z, Ma X, Jin Z, Xu Y, Zhang L. Single-center retrospective analysis of Pneumocystis jirovecii pneumonia in patients after deceased donor renal transplantation. Transpl Immunol 2022; 72:101593. [PMID: 35367619 DOI: 10.1016/j.trim.2022.101593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To investigate the clinical features, early diagnosis, and treatment methods of Pneumocystis jirovecii pneumonia (PJP) after renal transplantation (RT). METHODS We retrospectively analyzed the clinical data of 80 patients with confirmed PJP who underwent RT between 2018 and 2021 in our hospital. RESULTS In the present study, the incidence of PJP was 6.2% (80/1300). A 50% of cases (40 out of 80 patients) had developed a PJP infection during the first 6 months after RT and 81.3% (65 out of 80 patients) within 12 months. The median onset time of PJP was 6.5 months after RT. The most common symptom was fever (73.8%), followed by progressive dyspnea (51.3%) and dry cough (31.3%). In the initial phase of PJP, the most frequent CT finding was the presence of diffuse ground-grass shadows. In all, 27.5%, 37.5%, and 35% patients were diagnosed by induced sputum metagenomic next-generation sequencing (mNGS), peripheral blood mNGS, and characteristic clinical diagnostic features, respectively. The median 1,3-β-D-glucan level was 500 pg/mL, while the median C-reactive protein level was 63.4 mg/L. In most patients (83.8%), the procalcitonin levels were negative. The mean serum creatinine level was 171.9 ± 87.4 μmol/L. Of the 80 patients, 37 (46.2%) had coexisting cytomegalovirus (CMV) infection. All patients were treated with trimethoprim-sulfamethoxazole and third generation cephalosporin to prevent bacterial infection. The methylprednisolone dose (40-120 mg/d) varied according to illness. CONCLUSION PJP usually occurs within 1 year after RT, typically within 6 months. Fever, dry cough, and progressive dyspnea are the most common clinical symptoms. PJP should be highly suspected if the patient has clinical symptoms and diffuse, patchy, ground-glass opacities on CT in both lungs after RT within 1 year. Peripheral blood or induced sputum mNGS is helpful for early diagnosis of PJP. Trimethoprim-sulfamethoxazole is still the first choice for the treatment of PJP. Combined use of caspofungin can reduce the dose and adverse reactions of trimethoprim-sulfamethoxazole in theory.
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Affiliation(s)
- Jilin Zou
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Tianyu Wang
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Tao Qiu
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jiangqiao Zhou
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhongbao Chen
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Xiaoxiong Ma
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zeya Jin
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yu Xu
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Long Zhang
- Department of Organ Transplantation, Renmin Hospital of Wuhan University, Wuhan 430060, China.
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Tsang CC, Teng JLL, Lau SKP, Woo PCY. Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing. J Fungi (Basel) 2021; 7:jof7080636. [PMID: 34436175 PMCID: PMC8398552 DOI: 10.3390/jof7080636] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have recently developed beyond the research realm and started to mature into clinical applications. Here, we review the current use of NGS for laboratory diagnosis of fungal infections. Since the first reported case in 2014, >300 cases of fungal infections diagnosed by NGS were described. Pneumocystis jirovecii is the predominant fungus reported, constituting ~25% of the fungi detected. In ~12.5% of the cases, more than one fungus was detected by NGS. For P. jirovecii infections diagnosed by NGS, all 91 patients suffered from pneumonia and only 1 was HIV-positive. This is very different from the general epidemiology of P. jirovecii infections, of which HIV infection is the most important risk factor. The epidemiology of Talaromyces marneffei infection diagnosed by NGS is also different from its general epidemiology, in that only 3/11 patients were HIV-positive. The major advantage of using NGS for laboratory diagnosis is that it can pick up all pathogens, particularly when initial microbiological investigations are unfruitful. When the cost of NGS is further reduced, expertise more widely available and other obstacles overcome, NGS would be a useful tool for laboratory diagnosis of fungal infections, particularly for difficult-to-grow fungi and cases with low fungal loads.
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