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Tekin A, Truong HH, Rovati L, Lal A, Gerberi DJ, Gajic O, O’Horo JC. The Diagnostic Accuracy of Metagenomic Next-Generation Sequencing in Diagnosing Pneumocystis Pneumonia: A Systemic Review and Meta-analysis. Open Forum Infect Dis 2023; 10:ofad442. [PMID: 37674635 PMCID: PMC10478158 DOI: 10.1093/ofid/ofad442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
Background Pneumocystis pneumonia (PCP) is a growing concern as the immunocompromised population expands. Current laboratory approaches are limited. This systematic review aimed to evaluate metagenomic next-generation sequencing (MNGS) tests' performance in detecting PCP. Methods Five databases were searched through December 19, 2022, to identify original studies comparing MNGS with clinically diagnosed PCP. To assess the accuracy, symmetric hierarchical summary receiver operating characteristic models were used. Results Eleven observational studies reporting 1442 patients (424 with PCP) were included. Six studies focused exclusively on recipients of biologic immunosuppression (none with HIV-associated immunosuppression). Six were exclusively on bronchoalveolar lavage, while 1 was on blood samples. The sensitivity of MGNS was 0.96 (95% CI, 0.90-0.99), and specificity was 0.96 (95% CI, 0.92-0.98), with negative and positive likelihood ratios of 0.02 (95% CI, 0.01-0.05) and 19.31 (95% CI, 10.26-36.36), respectively. A subgroup analysis of studies exclusively including bronchoalveolar lavage (BAL) and blood samples demonstrated a sensitivity of 0.94 (95% CI, 0.78-0.99) and 0.93 (95% CI, 0.80-0.98) and a specificity of 0.96 (95% CI, 0.88-0.99) and 0.98 (95% CI, 0.76-1.00), respectively. The sensitivity analysis on recipients of biologic immunosuppression showed a sensitivity and specificity of 0.96 (95% CI, 0.90-0.98) and 0.94 (95% CI, 0.84-0.98), respectively. The overall confidence in the estimates was low. Conclusions Despite the low certainty of evidence, MNGS detects PCP with high sensitivity and specificity. This also applies to recipients of biologic immunosuppression and tests performed exclusively on blood samples without the need for BAL. Further studies are required in individuals with HIV-associated immunosuppression.
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Affiliation(s)
- Aysun Tekin
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Hong Hieu Truong
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Lucrezia Rovati
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Danielle J Gerberi
- Mayo Clinic Library Services, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, Minnesota, USA
| | - Ognjen Gajic
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - John C O’Horo
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
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Wang N, Gao Z, He S, Han M, Han W, Liu X, Cao H, Jing M, Sun T, Xu J. Lung abscess by Fusobacterium nucleatum and Streptococcus spp. co-infection by mNGS: A case series. Open Life Sci 2023; 18:20220651. [PMID: 37483431 PMCID: PMC10358748 DOI: 10.1515/biol-2022-0651] [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: 02/14/2023] [Revised: 05/15/2023] [Accepted: 06/05/2023] [Indexed: 07/25/2023] Open
Abstract
A lung abscess is a necrotizing infection caused by microbiomes that lead to the loss of healthy lung tissue. The routine culture is a waste of time and yields false-negative results, and clinicians could only choose empiric therapy or use broad-spectrum antibiotics, which could significantly contribute to the problem of resistance or aggravate the condition. We report three patients with a routine-culture-negative lung abscess. The presenting symptoms included fever, cough, dyspnea, and chest pain, and a computed tomography scan revealed a lesion in the lungs. The bronchoalveolar lavage fluid and pleural fluid were tested for pathogens using metagenome next-generation sequencing (mNGS), and the results revealed Fusobacterium nucleatum and Streptococcus spp. (S. constellatus, S. intermedius) as the most represented microbial pathogens. Our data demonstrated that mNGS could be a promising alternative diagnostic tool for pathogen detection, and the pathogen lists indicate that it will be important to focus on the Streptococcus genus rather than the dominant Streptococcus spp. in terms of co-infection of pathogen determined by shotgun mNGS.
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Affiliation(s)
- Na Wang
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Pharmacology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Zhichao Gao
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Breast Medicine, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Shuai He
- Department of Imaging, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Mengzhen Han
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Pharmacology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Wenjie Han
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Pharmacology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Xiaolin Liu
- Liaoning Kanghui Biotechnology Co., Ltd, Zhihuier Street, Hunnan District, Shenyang, 110001, China
| | - Hui Cao
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Breast Medicine, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Mingxi Jing
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Breast Medicine, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Tao Sun
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Breast Medicine, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
| | - Junnan Xu
- Department of Breast Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Pharmacology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Breast Medicine, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital, Shenyang, 110042, China
- Department of Medical Oncology, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital and Institute, No. 44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning110042, P. R. China
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Pan Y, Zhang X, Sun Y, Zhang Y, Bao W, Yin D, Zhang P, Zhang M. Cellular analysis and metagenomic next-generation sequencing of bronchoalveolar lavage fluid in the distinction between pulmonary non-infectious and infectious disease. Front Cell Infect Microbiol 2023; 12:1023978. [PMID: 36760236 PMCID: PMC9907085 DOI: 10.3389/fcimb.2022.1023978] [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: 08/20/2022] [Accepted: 12/15/2022] [Indexed: 01/26/2023] Open
Abstract
Background The aim of the current study was to investigate the clinical value of cellular analysis and metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in differentiating pulmonary non-infectious and infectious diseases in immunocompetent patients. Methods The present retrospective study was conducted from December 2017 to March 2020, and included immunocompetent patients with suspected pulmonary infection. High-resolution computed tomography, total cell counts and classification of BALF, conventional microbiological tests (CMTs), laboratory tests and mNGS of BALF were performed. Patients were assigned to pulmonary non-infectious disease (PNID) and pulmonary infectious disease (PID) groups based on final diagnoses. PNID-predictive values were analyzed via areas under receiver operating characteristic curves (AUCs). Optimal cutoffs were determined by maximizing the sum of sensitivity and specificity. Results A total of 102 patients suspected of pulmonary infection were enrolled in the study, 23 (22.5%) with PNID and 79 (77.5%) with PID. The diagnostic efficiency of BALF mNGS for differentiating PID from PNID was better than that of CMTs. Neutrophil percentage (N%) and the ratio of neutrophils to lymphocytes (N/L) in BALF were significantly lower in the PNID group than in the PID group. The AUCs for distinguishing PNID and PID were 0.739 (95% confidence interval [CI] 0.636-0.825) for BALF N%, 0.727 (95% CI 0.624-0.815) for BALF N/L, and 0.799 (95% CI 0.702-0.876) for BALF mNGS, with respective cutoff values of 6.7%, 0.255, and negative. Joint models of BALF mNGS combined with BALF N/L or BALF N% increased the respective AUCs to 0.872 (95% CI 0.786-0.933) and 0.871 (95% CI 0.784-0.932), which were significantly higher than those for BALF mNGS, BALF N%, and BALF N/L alone. Conclusions BALF N% ≤ 6.7% or BALF N/L ≤ 0.255 combined with a negative BALF mNGS result can effectively distinguish PNID from PID in immunocompetent patients with suspected pulmonary infection. BALF mNGS outperforms CMTs for identifying pathogens in immunocompetent patients, and the combination of mNGS and CMTs may be a better diagnostic strategy.
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Affiliation(s)
- Yilin Pan
- Department of Pulmonary and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xue Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Sun
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingying Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wuping Bao
- Department of Pulmonary and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongning Yin
- Department of Pulmonary and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pengyu Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Department of Infectious Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Min Zhang, ; Pengyu Zhang,
| | - Min Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Min Zhang, ; Pengyu Zhang,
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Foong KS, Mabayoje M, AlMajali A. Clinical Impact of Noninvasive Plasma Microbial Cell-Free Deoxyribonucleic Acid Sequencing for the Diagnosis and Management of Pneumocystis jirovecii Pneumonia: A Single-Center Retrospective Study. Open Forum Infect Dis 2022; 9:ofac652. [PMID: 36578518 PMCID: PMC9793099 DOI: 10.1093/ofid/ofac652] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
We present 23 cases of Pneumocystis jirovecii pneumonia (PCP) diagnosed with commercially available noninvasive plasma microbial cell-free deoxyribonucleic acid (mcfDNA) assay. Our findings suggest that plasma mcfDNA testing resulted in positive clinical impact for the diagnosis and treatment of PCP and coinfections in 82.6% of cases.
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Affiliation(s)
- Kap Sum Foong
- Correspondence: K. S. Foong, MD, Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, 800 Washington Street, Boston, MA 02111 ()
| | - Mojolaoluwa Mabayoje
- Department of Medicine, University of Illinois College of Medicine, Peoria, Illinois, USA
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Wang C, You Z, Fu J, Chen S, Bai D, Zhao H, Song P, Jia X, Yuan X, Xu W, Zhao Q, Pang F. Application of metagenomic next-generation sequencing in the diagnosis of pulmonary invasive fungal disease. Front Cell Infect Microbiol 2022; 12:949505. [PMID: 36237437 PMCID: PMC9551268 DOI: 10.3389/fcimb.2022.949505] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/05/2022] [Indexed: 12/16/2022] Open
Abstract
BackgroundMetagenomic next-generation sequencing (mNGS) is increasingly being used to detect pathogens directly from clinical specimens. However, the optimal application of mNGS and subsequent result interpretation can be challenging. In addition, studies reporting the use of mNGS for the diagnosis of invasive fungal infections (IFIs) are rare.ObjectiveWe critically evaluated the performance of mNGS in the diagnosis of pulmonary IFIs, by conducting a multicenter retrospective analysis. The methodological strengths of mNGS were recognized, and diagnostic cutoffs were determined.MethodsA total of 310 patients with suspected pulmonary IFIs were included in this study. Conventional microbiological tests (CMTs) and mNGS were performed in parallel on the same set of samples. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the logarithm of reads per kilobase per million mapped reads [lg(RPKM)], and read counts were used to predict true-positive pathogens.ResultThe majority of the selected patients (86.5%) were immunocompromised. Twenty species of fungi were detected by mNGS, which was more than was achieved with standard culture methods. Peripheral blood lymphocyte and monocyte counts, as well as serum albumin levels, were significantly negatively correlated with fungal infection. In contrast, C-reactive protein and procalcitonin levels showed a significant positive correlation with fungal infection. ROC curves showed that mNGS [and especially lg(RPKM)] was superior to CMTs in its diagnostic performance. The area under the ROC curve value obtained for lg(RPKM) in the bronchoalveolar lavage fluid of patients with suspected pulmonary IFIs, used to predict true-positive pathogens, was 0.967, and the cutoff value calculated from the Youden index was −5.44.ConclusionsIn this study, we have evaluated the performance of mNGS-specific indicators that can identify pathogens in patients with IFIs more accurately and rapidly than CMTs, which will have important clinical implications.
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Affiliation(s)
- Chengtan Wang
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Zhiqing You
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Juanjuan Fu
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Shuai Chen
- Department of Clinical Laboratory, Liaocheng Third People’s Hospital, Liaocheng, China
- Department of Virology, School of Public Health, Shandong University, Jinan, China
| | - Di Bai
- Department of Clinical Laboratory, Liaocheng Third People’s Hospital, Liaocheng, China
| | - Hui Zhao
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Pingping Song
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Xiuqin Jia
- The Key Laboratory of Molecular Pharmacology, Liaocheng People’s Hospital, Liaocheng, China
| | - Xiaoju Yuan
- Department of Gastroenterology, Liaocheng People’s Hospital, Liaocheng, China
| | - Wenbin Xu
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Qigang Zhao
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
- *Correspondence: Feng Pang, ; Qigang Zhao,
| | - Feng Pang
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
- *Correspondence: Feng Pang, ; Qigang Zhao,
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Chen S, Kang Y, Li D, Li Z. Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in patients with pulmonary infections: Systematic review and meta-analysis. Int J Infect Dis 2022; 122:867-873. [PMID: 35907477 DOI: 10.1016/j.ijid.2022.07.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022] Open
Abstract
BACKGROUND The identification of pathogens in patients with pulmonary infection has always been a major challenge in medicine. Compared with sputum and throat swabs, bronchoalveolar lavage fluid (BALF) can better reflect the actual state in the lungs. However, there has not been a meta-analysis of the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in detecting pathogens in BALF from patients with pulmonary infections. METHODS Data sources were PubMed, Web of Science, Embase, and the China National Knowledge Infrastructure. The pooled sensitivity and specificity were estimated by using random-effects or fixed-effect models. Subgroup analysis was performed to reveal the effect of potential explanatory factors on the diagnostic performance measures. RESULTS The pooled sensitivity was 78% (95% confidence interval: 67-87%; I2 = 92%) and the pooled specificity was 77% (95% confidence interval: 64-94%; I2 = 74%) for mNGS. Subgroup analyses for the sensitivity of mNGS revealed that patients with pulmonary infections who were severely ill or immunocompromised significantly affected heterogeneity (P < 0.001). The positive detection rate of mNGS for pathogens in BALF of severely or immunocompromised pulmonary-infected patients was 92% (95% confidence interval: 78-100%). CONCLUSION mNGS has high diagnostic performance for BALF pathogens in patients with pulmonary infections, especially in critically ill or immunocompromised patients.
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Affiliation(s)
- Shenglin Chen
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China; School of Public Health, Shanxi Medical University, 56 Xinjiannanlu Street, Taiyuan 030001, Shanxi, People's Republic of China
| | - Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China; School of Public Health, Shanxi Medical University, 56 Xinjiannanlu Street, Taiyuan 030001, Shanxi, People's Republic of China.
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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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Identification of Pneumocystis jirovecii with Fluorescence In-Situ Hybridization (FISH) in Patient Samples-A Proof-of-Principle. J Fungi (Basel) 2021; 8:jof8010013. [PMID: 35049953 PMCID: PMC8778293 DOI: 10.3390/jof8010013] [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: 12/06/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
In resource-limited settings, where pneumocystosis in immunocompromised patients is infrequently observed, cost-efficient, reliable, and sensitive approaches for the diagnostic identification of Pneumocystis jirovecii in human tissue samples are desirable. Here, an in-house fluorescence in situ hybridization assay was comparatively evaluated against Grocott’s staining as a reference standard with 30 paraffin-embedded tissue samples as well as against in-house real-time PCR with 30 respiratory secretions from immunocompromised patients with clinical suspicion of pneumocystosis. All pneumocystosis patients included in the study suffered from HIV/AIDS. Compared with Grocott’s staining as the reference standard, sensitivity of the FISH assay was 100% (13/13), specificity was 41% (7/17), and the overall concordance was 66.7% with tissue samples. With respiratory specimens, sensitivity was 83.3% (10/12), specificity was 100% (18/18), and the overall concordance was 93.3% as compared with real-time PCR. It remained unresolved to which proportions sensitivity limitations of Grocott’s staining or autofluorescence phenomena affecting the FISH assay accounted for the recorded reduced specificity with the tissue samples. The assessment confirmed Pneumocystis FISH in lung tissue as a highly sensitive screening approach; however, dissatisfying specificity in paraffin-embedded biopsies calls for confirmatory testing with other techniques in case of positive FISH screening results. In respiratory secretions, acceptable sensitivity and excellent specificity were demonstrated for the diagnostic application of the P. jirovecii-specific FISH assay.
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