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Wu H, Cao H, Gao X, Shi C, Wang L, Gao B. The role of metagenomic next-generation sequencing in diagnosing and managing post-kidney transplantation infections. Front Cell Infect Microbiol 2025; 14:1473068. [PMID: 39839264 PMCID: PMC11747774 DOI: 10.3389/fcimb.2024.1473068] [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: 07/30/2024] [Accepted: 12/16/2024] [Indexed: 01/23/2025] Open
Abstract
Kidney transplantation (KT) is a life-saving treatment for patients with end-stage renal disease, but post-transplant infections remain one of the most significant challenges. These infections, caused by a variety of pathogens, can lead to prolonged hospitalization, graft dysfunction, and even mortality, particularly in immunocompromised patients. Traditional diagnostic methods often fail to identify the causative organisms in a timely manner, leading to delays in treatment and poorer patient outcomes. This review explores the application of metagenomic next-generation sequencing (mNGS) in the diagnosis of post-KT infections. mNGS allows for the rapid, comprehensive detection of a wide range of pathogens, including bacteria, viruses, fungi, and parasites, without the need for culture-based techniques. We discuss the advantages of mNGS in early and accurate pathogen identification, its role in improving patient management, and the potential challenges in its clinical implementation. Additionally, we consider the future prospects of mNGS in overcoming current diagnostic limitations and its potential for guiding targeted therapies, particularly in detecting antimicrobial resistance and emerging pathogens. This review emphasizes the promise of mNGS as an essential tool in improving the diagnosis and treatment of infections in KT recipients.
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Affiliation(s)
| | | | | | | | | | - Baoshan Gao
- Department of Urology II, The First Hospital of Jilin University, Changchun, China
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Gao C, Wei G, Zhang C, Wang C, Li C, Li R, Su Z, Zheng Z. Pneumocystis jirovecii pneumonia increases the 3-months mortality of anti-MDA5-antibody-positive dermatomyositis patients. Front Immunol 2024; 15:1504380. [PMID: 39669577 PMCID: PMC11634837 DOI: 10.3389/fimmu.2024.1504380] [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: 09/30/2024] [Accepted: 11/13/2024] [Indexed: 12/14/2024] Open
Abstract
Background Anti-melanoma differentiation-associated gene 5 antibody-positive dermatomyositis (anti-MDA5+DM) patients are associated with considerable mortality, and opportunistic infections including Pneumocystis jirovecii pneumonia (PJP)is the main cause. This study was to identify clinical characteristics, risk factors, and prognostic factors of PJP diagnosed by bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in anti-MDA5+ DM patients. Methods In this retrospective observational study, all patients admitted with suspected pneumonia were detected for mNGS in BALF. The demographics, comorbidities, laboratory parameters, and treatments of the patients were compared and analyzed in both groups to identify the potential risk factors for PJP and death via Logistic regression and Cox proportional hazards regression, respectively. Results Overall, 92 patients were included in this study, 46(50.0%) were defined as PJP+ group, and the other 46 (50.0%) as PJP- group, and 31(67.4%) PJP occurred in the first 3 months. Increased neutrophil-lymphocyte ratio (NLR) and CRP were independent risk factors for PJP occurrence, while trimethoprim-sulfamethoxazole (TMP/SMZ) prophylaxis was an independent protective factor (all p<0.05). The three-months mortality rate was higher in the PJP+ group compared to PJP- group (43.5% vs 23.9%, p=0.047). Rapidly progressive interstitial lung disease (RPILD) was a main predictor of mortality in anti-MDA5+DM patients with PJP, whereas glucocorticoid use was a significant protective factor. Conclusions PJP has high prevalence and mortality in anti-MDA5+DM, while TMP/SMZ prophylaxis significantly reduces PJP risk. Mortality in PJP+ patients is primarily concentrated within the first 3 months, associated with RPILD. Early intervention with corticosteroids and prophylactic measures are crucial in reducing mortality.
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Affiliation(s)
- Congcong Gao
- Department of Rheumatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gaohui Wei
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunyi Zhang
- Department of Rheumatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chenqiong Wang
- Department of Rheumatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chaoying Li
- Department of Rheumatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruxu Li
- Department of Rheumatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhaohui Su
- Department of Rheumatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhaohui Zheng
- Department of Rheumatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Cai R, Yu F, Cheng J, Chen C, Liu Y, Lv R, Ye Z, Yuan Y, Li Z, Cheng C, Wei H. Diagnostic Value of Metagenomic next-generation sequencing and X-pert in Bronchoalveolar lavage fluid for pneumonia in HIV-infected and HIV-uninfected patients. Heliyon 2024; 10:e38208. [PMID: 39386812 PMCID: PMC11462377 DOI: 10.1016/j.heliyon.2024.e38208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 09/18/2024] [Accepted: 09/19/2024] [Indexed: 10/12/2024] Open
Abstract
Background The pathogens causing unexplained pneumonia in both HIV-infected or HIV-unfected patients are likely to be complex. This retrospective study aimed to characterize the etiology of pneumonia in HIV-infected and HIV-uninfected patients using bronchoalveolar lavage fluid (BALF) analysis with metagenomic next-generation sequencing (mNGS) and X-pert MTB/RIF. Methods Between January 2022 and May2024, 141 HIV-infected and 104 HIV-uninfected patients admitted to Nanjing Second Hospital with pneumonia were included. BALF samples were collected and analyzed using mNGS to detect bacteria, fungi, viruses, tuberculosis (TB) and non-tuberculous mycobacteria (NTM), and X-pert for TB detection. Clinical data including CD4 T-cell counts, comorbidities, and ART status were collected and analyzed. Results HIV-uninfected patients were found to be older and exhibited a higher prevalence of comorbidities compared to HIV-infected patients. Despite higher median CD4 T-cell counts in HIV-uninfected individuals (412 cells/μL vs. 31 cells/μL in HIV-infected), TB detection rates using X-pert and mNGS were lower than anticipated, particularly in HIV-infected patients. Mixed-pathogen infections were significantly more prevalent in HIV-infected patients, especially those with lower CD4 T-cell counts. ART use showed variable impacts on pathogen diversity, with longer treatment durations associated with reduced infection complexity but persistent immunodeficiency in some cases.In patients with pneumonia, whether HIV-infected or HIV-uninfected, pathogens often exhibit complexity, underscoring the critical role of timely mNGS and X-pert analysis of BALF for early pathogen detection.
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Affiliation(s)
- Rentian Cai
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, 210003, Nanjing, No. 1-1, Zhongfu road, China
| | - Fengxue Yu
- Department of Radiotherapy, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, 210003, Nanjing, No. 1-1, Zhongfu road, China
| | - Jian Cheng
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, 210003, Nanjing, No. 1-1, Zhongfu road, China
| | - Chen Chen
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, 210003, Nanjing, No. 1-1, Zhongfu road, China
| | - Yuan Liu
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, 210003, Nanjing, No. 1-1, Zhongfu road, China
| | - Ru Lv
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, 210003, Nanjing, No. 1-1, Zhongfu road, China
| | - Zi Ye
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, 210003, Nanjing, No. 1-1, Zhongfu road, China
| | - Yin Yuan
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, 210003, Nanjing, No. 1-1, Zhongfu road, China
| | - Zhengjie Li
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, 210003, Nanjing, No. 1-1, Zhongfu road, China
| | - Cong Cheng
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, 210003, Nanjing, No. 1-1, Zhongfu road, China
| | - Hongxia Wei
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, 210003, Nanjing, No. 1-1, Zhongfu road, China
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Qin Y, Zou X, Jin Y, Li J, Cai Q. Cryptococcus Neoformans Osteomyelitis of the Right Ankle Diagnosed by Metagenomic Next-Generation Sequencing in a HIV-Negative Patient with Tuberculous Lymphadenitis and Pulmonary Tuberculosis: A Case Report and Recent Literature Review. Infect Drug Resist 2024; 17:3805-3812. [PMID: 39253606 PMCID: PMC11381933 DOI: 10.2147/idr.s476270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/09/2024] [Indexed: 09/11/2024] Open
Abstract
Aim Cryptococcus neoformans osteomyelitis coupled with tuberculosis and tuberculous lymphadenitis, is a rare occurrence in clinical. Diagnostic challenges arise due to the clinical radiological similarity of this condition to other lung infections and the limited and sensitive nature of traditional approaches. Here, we present a case of co-infection diagnosed using Metagenomic Next-Generation Sequencing, highlighting the effectiveness of advanced genomic techniques in such complex scenarios. Case Presentation We present a case of a 67-year-old female infected with cryptococcal osteomyelitis and presented with swelling and pain in the right ankle. Following a biopsy of the right ankle joint, Metagenomic Next-Generation Sequencing (mNGS) of the biopsy tissue revealed Cryptococcus neoformans infection. Positive results for Cryptococcus capsular antigen and pathological findings confirmed the presence of Cryptococcus neoformans. The patient underwent surgical debridement, coupled with oral fluconazole treatment (300mg/day), leading to the resolution of symptoms. Conclusion Cryptococcus neoformans is an uncommon cause of ankle infection. Metagenomic Next-Generation Sequencing (mNGS) serves as a valuable diagnostic tool, aiding clinicians in differentiating cryptococcal osteomyelitis from other atypical infections.
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Affiliation(s)
- Yao Qin
- Department of Tuberculosis, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Xingwu Zou
- Department of Tuberculosis, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Yanghui Jin
- Department of Orthopaedic, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Jinmeng Li
- Department of Pharmacy, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Qingshan Cai
- Department of Tuberculosis, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
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Hu X, Jiang L, Liu X, Chang H, Dong H, Yan J, Zhou X, Kong M. The diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in critically ill patients with respiratory tract infections. Microbiol Spectr 2024; 12:e0045824. [PMID: 38916357 PMCID: PMC11302328 DOI: 10.1128/spectrum.00458-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 05/18/2024] [Indexed: 06/26/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is an unbiased and rapid method for detecting pathogens. This study enrolled 145 suspected severe pneumonia patients who were admitted to the Affiliated Hospital of Jining Medical University. This study primarily aimed to determine the diagnostic performance of mNGS and conventional microbiological tests (CMTs) using bronchoalveolar lavage fluid samples for detecting pathogens. Our findings indicated that mNGS performed significantly higher sensitivity (97.54% vs 28.68%, P < 0.001), coincidence (90.34% vs 35.17%, P < 0.001), and negative predictive value (80.00% vs 13.21%, P < 0.001) but performed lower specificity than CMTs (52.17% vs 87.5%, P < 0.001). Streptococcus pneumoniae as the most common bacterial pathogen had the largest proportion (22.90%, 30/131) in this study. In addition to bacteria, fungi, and virus, mNGS can detect a variety of atypical pathogens such as Mycobacterium tuberculosis and non-tuberculous. Mixed infections were common in patients with severe pneumonia, and bacterial-fungal-viral-atypical pathogens were the most complicated infection. After adjustments of antibiotics based on mNGS and CMTs, the clinical manifestation improved in 139 (95.86%, 139/145) patients. Our data demonstrated that mNGS had significant advantage in diagnosing respiratory tract infections, especially atypical pathogens and fungal infections. Pathogens were detected timely and comprehensively, contributing to the adjustments of antibiotic treatments timely and accurately, improving patient prognosis and decreasing mortality potentially.IMPORTANCEMetagenomic next-generation sequencing using bronchoalveolar lavage fluid can provide more comprehensive and accurate pathogens for respiratory tract infections, especially when considering the previous usage of empirical antibiotics before admission or complicated clinical presentation. This technology is expected to play an important role in the precise application of antimicrobial drugs in the future.
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Affiliation(s)
- Xiaohang Hu
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Liqing Jiang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaowei Liu
- Department of Intensive Care Unit, Affiliated Hospital of Jining Medical University,Jining Medical University, Shandong Jining, China
| | - Hong Chang
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Haixin Dong
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Jinyan Yan
- Medical Laboratory Science, Affiliated Hospital of Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Xiaoya Zhou
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
| | - Min Kong
- Medical Laboratory of Jining Medical University, Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical University, Jining Medical University, Shandong Jining, China
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Liu Z, Chen H, Chen D, Wu X, Xu H, Chen P, Wang R, Chen Y. Metagenomic next-generation sequencing for the diagnosis of invasive pulmonary aspergillosis in type 2 diabetes mellitus patients. Sci Rep 2024; 14:16618. [PMID: 39025875 PMCID: PMC11258266 DOI: 10.1038/s41598-024-67174-8] [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: 03/18/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
Invasive pulmonary aspergillosis (IPA) in patients with diabetes mellitus has high incidence, especially in Type 2 diabetes mellitus (T2DM). The aim of this study was to evaluate the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) for IPA in patients with T2DM. A total of 66 patients with T2DM were included, including 21 IPA and 45 non-IPA patients, from January 2022 to December 2022. The demographic characteristics, comorbidities, laboratory test results, antibiotic treatment response, and 30-day mortality rate of patients were analyzed. The diagnostic accuracy of mNGS and conventional methods was compared, including sensitivity, specificity, positive predictive value and negative predictive value. The sensitivity and specificity of mNGS were 66.7% and 100.0%, respectively, which were significantly higher than those of fluorescence staining (42.1% and 100%), serum 1,3-β-D-glucan detection (38.1% and 90.9%), serum galactomannan detection (14.3% and 94.9%) and BALF galactomannan detection (47.3% and 70.7%). Although the sensitivity of BALF culture (75.0%) was higher than that of mNGS (66.7%), the turnover time of mNGS was significantly shorter than that of traditional culture (1.6 days vs. 5.0 days). The sensitivity of mNGS combined with BALF culture reached 100.0%. In addition, mNGS has a stronger ability to detect co-pathogens with IPA. 47.6% of T2DM patients with IPA were adjusted the initial antimicrobial therapy according to the mNGS results. This is the first study to focus on the diagnostic performance of mNGS in IPA infection in T2DM patients. MNGS can be used as a supplement to conventional methods for the diagnosis of IPA in patients with T2DM.
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Affiliation(s)
- Zhiyun Liu
- Department of Clinical Laboratory, Huizhou Central People's Hospital, Huizhou, 516001, Guangdong, China
| | - Hengxin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Dubo Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Xianjin Wu
- Department of Clinical Laboratory, Huizhou Central People's Hospital, Huizhou, 516001, Guangdong, China
| | - Hongxu Xu
- 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
| | - Ruizhi Wang
- 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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Zhang Z, Liu T, Ming M, Shen M, Zhang Y, Chen H, Chen W, Tao J, Wang Y, Liu J, Zhou J, Lu G, Yan G. Metagenomic next-generation sequencing promotes diagnosis and treatment of Pneumocystis jirovecii pneumonia in non-HIV infected children: a retrospective study. BMC Pulm Med 2024; 24:338. [PMID: 38997717 PMCID: PMC11241876 DOI: 10.1186/s12890-024-03135-1] [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: 08/23/2023] [Accepted: 06/27/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) excels in diagnosis of infection pathogens. We aimed to evaluate the performance of mNGS for the diagnosis of Pneumocystis jirovecii pneumonia (PJP) in non-HIV infected children. METHODS Totally 36 PJP children and 61 non-PJP children admitted to the pediatric intensive care unit from March 2018 to December 2021 were retrospectively enrolled. Clinical features of PJP children were summarized. 1,3-β-D glucan (BDG) test and bronchoalveolar lavage fluid (BALF) mNGS were used for evaluation of PJP diagnostic performance. Antimicrobial management modifications for PJP children after the mNGS results were also reviewed. RESULTS Pneumocystis jirovecii was detected in all PJP children by mNGS (36/36), and the sensitivity of mNGS was 100% (95% confidence interval [CI]: 90.26-100%). The sensitivity of BDG was 57.58% (95% CI: 39.22-74.52%). Of the 26 (72.2%) PJP patients with mixed infection, twenty-four (66.7%) were detected by BALF-mNGS. Thirteen patients (36.1%) had their antimicrobial management adjusted according to the mNGS results. Thirty-six PJP children included 17 (47.2%) primary immunodeficiency and 19 (52.8%) secondary immunodeficiency, of whom 19 (52.8%) survived and 17 (47.2%) died. Compared to survival subgroup, non-survival subgroup had a higher rate of primary immunodeficiency (64.7% vs. 31.6%, P = 0.047), younger age (7 months vs. 39 months, P = 0.011), lower body weight (8.0 kg vs. 12.0 kg, P = 0.022), and lower T lymphocyte counts. CONCLUSIONS The mortality rate of PJP in immunosuppressed children without HIV infection is high and early diagnosis is challenging. BALF-mNGS could help identify PJP and guide clinical management.
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Affiliation(s)
- Zhenyu Zhang
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, No.399 Wanyuan Rd., Minhang Dist., Shanghai, 201102, China
| | - Tingyan Liu
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, No.399 Wanyuan Rd., Minhang Dist., Shanghai, 201102, China
| | - Meixiu Ming
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, No.399 Wanyuan Rd., Minhang Dist., Shanghai, 201102, China
| | - Meili Shen
- Medical Department, Nanjing Dinfectome Technology Inc., Nanjing, China
| | - Yi Zhang
- Department of Clinical Epidemiology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Hanlin Chen
- Medical Department, Nanjing Dinfectome Technology Inc., Nanjing, China
| | - Weiming Chen
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, No.399 Wanyuan Rd., Minhang Dist., Shanghai, 201102, China
| | - Jinhao Tao
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, No.399 Wanyuan Rd., Minhang Dist., Shanghai, 201102, China
| | - Yixue Wang
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, No.399 Wanyuan Rd., Minhang Dist., Shanghai, 201102, China
| | - Jing Liu
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, No.399 Wanyuan Rd., Minhang Dist., Shanghai, 201102, China
| | - Jihua Zhou
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, No.399 Wanyuan Rd., Minhang Dist., Shanghai, 201102, China
| | - Guoping Lu
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, No.399 Wanyuan Rd., Minhang Dist., Shanghai, 201102, China.
| | - Gangfeng Yan
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, No.399 Wanyuan Rd., Minhang Dist., Shanghai, 201102, China.
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Pham D, Sivalingam V, Tang HM, Montgomery JM, Chen SCA, Halliday CL. Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches. J Fungi (Basel) 2024; 10:447. [PMID: 39057332 PMCID: PMC11278267 DOI: 10.3390/jof10070447] [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: 05/31/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Invasive fungal diseases (IFDs) comprise a growing healthcare burden, especially given the expanding population of immunocompromised hosts. Early diagnosis of IFDs is required to optimise therapy with antifungals, especially in the setting of rising rates of antifungal resistance. Molecular techniques including nucleic acid amplification tests and whole genome sequencing have potential to offer utility in overcoming limitations with traditional phenotypic testing. However, standardisation of methodology and interpretations of these assays is an ongoing undertaking. The utility of targeted Aspergillus detection has been well-defined, with progress in investigations into the role of targeted assays for Candida, Pneumocystis, Cryptococcus, the Mucorales and endemic mycoses. Likewise, whilst broad-range polymerase chain reaction assays have been in use for some time, pathology stewardship and optimising diagnostic yield is a continuing exercise. As costs decrease, there is also now increased access and experience with whole genome sequencing, including metagenomic sequencing, which offers unparalleled resolution especially in the investigations of potential outbreaks. However, their role in routine diagnostic use remains uncommon and standardisation of techniques and workflow are required for wider implementation.
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Affiliation(s)
- David Pham
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Varsha Sivalingam
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Helen M. Tang
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - James M. Montgomery
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Catriona L. Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Westmead, NSW 2145, Australia; (D.P.)
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Wang C, Yin X, Ma W, Zhao L, Wu X, Ma N, Cao Y, Zhang Q, Ma S, Xu L, Wang X. Clinical application of bronchoalveolar lavage fluid metagenomics next-generation sequencing in cancer patients with severe pneumonia. Respir Res 2024; 25:68. [PMID: 38317206 PMCID: PMC10840150 DOI: 10.1186/s12931-023-02654-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/25/2023] [Indexed: 02/07/2024] Open
Abstract
OBJECTIVE Metagenomic next-generation sequencing (mNGS), as an emerging technique for pathogen detection, has been widely used in clinic. However, reports on the application of mNGS in cancer patients with severe pneumonia remain limited. This study aims to evaluate the diagnostic performance of bronchoalveolar lavage fluid (BALF) mNGS in cancer patients complicated with severe pneumonia. METHODS A total of 62 cancer patients with severe pneumonia simultaneously received culture and mNGS of BALF were enrolled in this study. We systematically analyzed the diagnostic significance of BALF mNGS. Subsequently, optimization of anti-infective therapy based on the distribution of pathogens obtained from BALF mNGS was also assessed. RESULTS For bacteria and fungi, the positive detection rate of mNGS was significantly higher than culture method (91.94% versus 51.61%, P < 0.001), especially for poly-microbial infections (70.97% versus 12.90%, P < 0.001). Compared with the culture method, mNGS exhibited a diagnostic sensitivity of 100% and a specificity of 16.67%, with the positive predictive value (PPV) and negative predictive value (NPV) being 56.14% and 100%, respectively. The agreement rate between these two methods was 59.68%, whereas kappa consensus analysis indicated a poor concordance (kappa = 0.171). After receipt of BALF mNGS results, anti-infective treatment strategies in 39 out of 62 cases (62.90%) were optimized. Moreover, anti-tumor therapy was a high-risk factor for mixed infections (87.18% versus 65.22%, P = 0.04). CONCLUSIONS The present study showed that cancer patients with severe pneumonia, especially those received anti-tumor therapy, were more likely to have poly-microbial infections. BALF mNGS can provide a rapid and comprehensive pathogen distribution of pulmonary infection, making it a promising technique in clinical practice, especially for optimizing therapeutic strategies for cancer patients.
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Affiliation(s)
- Chao Wang
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Xiaojuan Yin
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Wenqing Ma
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Li Zhao
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Xuhong Wu
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Nan Ma
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Yuepeng Cao
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Quanli Zhang
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, Jiangsu, 210009, China
| | - Shuliang Ma
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Lin Xu
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China.
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, Jiangsu, 210009, China.
| | - Xuerong Wang
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China.
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Fu R, Lin R, Fan ZP, Huang F, Xu N, Xuan L, Huang YF, Liu H, Zhao K, Wang ZX, Jiang L, Dai M, Sun J, Liu QF. [Metagenomic next-generation sequencing for the diagnosis of Pneumocystis jirovecii pneumonia after allogeneic hematopoietic stem cell transplantation]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2024; 45:62-67. [PMID: 38527840 PMCID: PMC10951114 DOI: 10.3760/cma.j.cn121090-20230928-00147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Indexed: 03/27/2024]
Abstract
Objectives: To investigate the value of metagenomic next-generation sequencing (mNGS) in the diagnosis of Pneumocystis jirovecii pneumonia (PJP) in patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) . Methods: The data of 98 patients with suspected pulmonary infection after allo-HSCT who underwent pathogen detection from bronchoalveolar lavage fluid between June 2016 and August 2023 at Nanfang Hospital were analyzed. The diagnostic performance of mNGS, conventional methods, and real-time quantitative polymerase chain reaction (qPCR) for PJP were compared. Results: A total of 12 patients were diagnosed with PJP, including 11 with a proven diagnosis and 1 with a probable diagnosis. Among the patients with a proven diagnosis, 1 was positive by both conventional methods and qPCR, and 10 were positive by qPCR only. Pneumocystis jirovecii was detected by mNGS in all 12 patients. The diagnostic sensitivity of mNGS for PJP was 100%, which was greater than that of conventional methods (8.3%, P=0.001) and similar to that of qPCR (91.6%, P=1.000) . A total of 75% of the patients developed mixed pulmonary infections, and cytomegalovirus and Epstein-Barr virus were the most common pathogens. Mixed infection was detected in eight patients by mNGS and in five patients by qPCR, but not by conventional methods (P=0.008) . Conclusions: mNGS had good sensitivity for diagnosing PJP after allo-HSCT and was advantageous for detecting mixed infectious pathogens; therefore, mNGS might be an effective supplement to regular detection methods and qPCR.
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Affiliation(s)
- R Fu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - R Lin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - Z P Fan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - F Huang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - N Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - L Xuan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - Y F Huang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - H Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - K Zhao
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - Z X Wang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - L Jiang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - M Dai
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - J Sun
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
| | - Q F Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou 510515, China
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Chen X, Shu X, He L, Yang H, Lu X, Wang G, Ge Y. High prevalence and mortality of Pneumocystis jirovecii pneumonia in anti-MDA5 antibody-positive dermatomyositis. Rheumatology (Oxford) 2023; 62:3302-3309. [PMID: 36734589 DOI: 10.1093/rheumatology/kead063] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/15/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVES To identify potential risk factors and prognostic factors of Pneumocystis jirovecii pneumonia (PJP) infection in anti-melanoma differentiation-associated gene 5 antibody-positive DM (anti-MDA5+ DM) patients, and to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS). METHODS Anti-MDA5+ DM patients who underwent mNGS or real-time PCR for PJP detection were recruited. The potential risk factors for PJP occurrence and death were analysed via Logistic regression and Cox proportional hazards regression, respectively. The diagnostic efficacy of mNGS was compared with the conventional methods. RESULTS 91 patients were enrolled and 44 were assigned to PJP+ group. The PJP detection rate was 48.4%. PJP often occurred in the first 3 months (68.2%) of the disease; this period also showed the highest mortality rate (20.5%). Fever and increased lactate dehydrogenase (LDH) were independent risk factors for PJP occurrence, while trimethoprim-sulfamethoxazole (TMP/SMZ) prophylaxis was an independent protective factor (all P < 0.05). Older age and increased LDH were predictors for mortality in patients with anti-MDA5+ DM and PJP (all P < 0.05). In addition, we found that mNGS had a sensitivity of 100.0% and specificity of 90.0% in diagnosing PJP, with the highest area under the curve of 0.95 (P < 0.001). CONCLUSION PJP has high prevalence and mortality in anti-MDA5+ DM. It is crucial for clinicians to identify high-risk patients and promptly institute TMP/SMZ to prevent PJP. mNGS is the preferred approach for pathogen detection in anti-MDA5+ DM when PJP is suspected.
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Affiliation(s)
- Xixia Chen
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Xiaoming Shu
- Department of Rheumatology, Key Myositis Laboratories, China-Japan Friendship Hospital, Beijing, China
| | - Linrong He
- Department of Rheumatology, Key Myositis Laboratories, China-Japan Friendship Hospital, Beijing, China
| | - Hanbo Yang
- Department of Rheumatology, Key Myositis Laboratories, China-Japan Friendship Hospital, Beijing, China
| | - Xin Lu
- Department of Rheumatology, Key Myositis Laboratories, China-Japan Friendship Hospital, Beijing, China
| | - Guochun Wang
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
- Department of Rheumatology, Key Myositis Laboratories, China-Japan Friendship Hospital, Beijing, China
| | - Yongpeng Ge
- Department of Rheumatology, Key Myositis Laboratories, China-Japan Friendship Hospital, Beijing, China
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12
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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: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [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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Li X, Li Z, Ye J, Ye W. Diagnostic performance of metagenomic next-generation sequencing for Pneumocystis jirovecii pneumonia. BMC Infect Dis 2023; 23:455. [PMID: 37430211 PMCID: PMC10331973 DOI: 10.1186/s12879-023-08440-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023] Open
Abstract
OBJECTIVE Pneumocystis jirovecii pneumonia (PJP) can be a life-threatening opportunistic infection. We aimed to evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for PJP. METHODS A comprehensive electronic literature search of Web of Knowledge, PubMed, Cochrane Library, CNKI and Wanfang data was performed. Bivariate analysis was conducted to calculate the pooled sensitivity, specificity, diagnostic odds ratio (DOR), the area under the summary receiver operator characteristic (SROC) curve and the Q-point value (Q*). RESULTS The literature search resulted in 9 studies with a total of 1343 patients, including 418 cases diagnosed with PJP and 925 controls. The pooled sensitivity of mNGS for diagnosis of PJP was 0.974 [95% confidence interval (CI), 0.953-0.987]. The pooled specificity was 0.943 (95% CI, 0.926-0.957), the DOR was 431.58 (95% CI, 186.77-997.27), the area under the SROC curve was 0.987, and the Q* was 0.951. The I2 test indicated no heterogeneity between studies. The Deek funnel test suggested no potential publication bias. Subgroup analyses showed that the area under the SROC curve of mNGS for diagnosis of PJP in immunocompromised and non-HIV patients was 0.9852 and 0.979, respectively. CONCLUSIONS Current evidence indicates that mNGS exhibits excellent accuracy for the diagnosis of PJP. The mNGS is a promising tool for assessment of PJP in both immunocompromised and non-HIV patients.
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Affiliation(s)
- Xuefang Li
- Department of Infectious Diseases, Zhejiang Hospital, 1229 Gudun Road, Xihu District, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Zhijun Li
- Department of Respiratory Diseases, Zhejiang Hospital, 1229 Gudun Road, Xihu District, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Jian Ye
- Department of Respiratory Diseases, Zhejiang Hospital, 1229 Gudun Road, Xihu District, Hangzhou, 310013, Zhejiang Province, People's Republic of China
| | - Wu Ye
- Department of Respiratory Diseases, Zhejiang Hospital, 1229 Gudun Road, Xihu District, Hangzhou, 310013, Zhejiang Province, People's Republic of China.
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14
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Huang JJ, Zhang SS, Liu ML, Yang EY, Pan Y, Wu J. Next-generation sequencing technology for the diagnosis of Pneumocystis pneumonia in an immunocompetent female: A case report. World J Clin Cases 2023; 11:4425-4432. [PMID: 37449225 PMCID: PMC10337001 DOI: 10.12998/wjcc.v11.i18.4425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND Pneumocystis pneumonia (PCP) is a serious fungal infection usually seen in patients with human immunodeficiency virus, and it is more frequently found and has a high fatality rate in immunocompromised people. Surprisingly, it rarely occurs in immunocompetent patients. However, the clinical diagnosis of this pathogen is made more difficult by the difficulty of obtaining accurate microbiological evidence with routine tests. This case reports a PCP patient with normal immune function who was diagnosed through next-generation sequencing (NGS).
CASE SUMMARY A 23-year-old female who had no special disease in the past was admitted to the hospital with a persistent fever and cough. Based on the initial examination results, the patient was diagnosed with bipulmonary pneumonia, and empirical broad-spectrum antibiotic therapy was administered. However, due to the undetermined etiology, the patient's condition continued to worsen. She was transferred to the intensive care unit because of acute respiratory failure. After the diagnosis of Pneumocystis jirovecii infection through NGS in bronchoalveolar lavage fluid and treatment with trimethoprim/sulfamethoxazole and caspofungin, the patient gradually recovered and had a good prognosis.
CONCLUSION This case emphasizes that, for patients with normal immune function the possibility of PCP infection, although rare, cannot be ignored. NGS plays an important role in the diagnosis of refractory interstitial pneumonia and acute respiratory failure.
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Affiliation(s)
- Jing-Ji Huang
- The Second Clinical Medical College, Guizhou University of Traditional Chinese Medicine, Guiyang 550000, Guizhou Province, China
| | - Song-Song Zhang
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang 550000, Guizhou Province, China
| | - Man-Li Liu
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang 550000, Guizhou Province, China
| | - En-Yu Yang
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang 550000, Guizhou Province, China
| | - Yu Pan
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang 550000, Guizhou Province, China
| | - Jing Wu
- Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang 550000, Guizhou Province, China
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Sun H, Chen R, Li T, Gao J, Gu X, Zhu X, Jin L, Shi Y, Li Q. Combination of transbronchial cryobiopsy based clinic-radiologic-pathologic strategy and metagenomic next-generation sequencing for differential diagnosis of rapidly progressive diffuse parenchymal lung diseases. Front Cell Infect Microbiol 2023; 13:1204024. [PMID: 37408612 PMCID: PMC10318139 DOI: 10.3389/fcimb.2023.1204024] [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: 04/11/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023] Open
Abstract
Background The complicated spectrum of rapidly progressive diffused parenchymal lung diseases (RP-DPLD) creates obstacles to the precise diagnosis and treatment. We evaluated the differential diagnostic value of transbronchial cryobiopsy (TBCB) based clinic-radiologic-pathologic (CRP) strategy combined with bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in RP-DPLD patients. Methods RP-DPLD patients who underwent the diagnostic strategy of TBCB-based CRP combined with BALF mNGS at Shanghai East Hospital from May 2020 to Oct 2022 were retrospectively analyzed. Clinical characteristics were summarized, including demographic data, high-resolution computed tomography (HRCT) findings, histopathology of TBCB and microbiological results. Diagnostic value of the combined strategy, as well as the sensitivity, specificity, and positive detection rates of mNGS were evaluated. Results A total of 115 RP-DPLD patients were enrolled, with a mean age of 64.4 years old and a male proportion of 54.8%. The pulmonary imaging findings in most patients were complex and diverse, with all patients showing bilateral lung diffuse lesions in HRCT, and progressively aggravated imaging changes within one month. After combining TBCB-based CRP strategy with mNGS, all participants received a corresponding diagnosis with 100% diagnostic yield. In these patients, 58.3% (67/115) were diagnosed with noninfectious RP-DPLD and 41.7% (48/115) with infection-related RP-DPLD. There were 86.1% of cases with known etiology according to the DPLD classification. BALF mNGS and traditional pathogen detection methods were performed in all patients, the positive detection rates were 50.4% (58/115) and 32.2% (37/115), respectively. Meanwhile, the mNGS showed significantly higher sensitivity and negative predictive value than the traditional pathogen detection methods for the diagnosis of infection-related RP-DPLD (100% vs 60.4% (p<0.001), 100% vs 75.6% (p<0.001), respectively). Among noninfectious RP-DPLD patients, the true negative rate of mNGS was 85.1% (57/67). All patients had their treatment regimen modified and the 30-day mortality was 7.0%. Conclusion The novel strategy of TBCB-based CRP combined with mNGS provided dependable and sufficient evidence for the diagnosis, meanwhile further improved the accuracy of RP-DPLD treatment, as well as the prognosis of patients. Our results highlight the significant value of combined strategy in determining whether the RP-DPLD patients were infection associated or not.
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Affiliation(s)
- He Sun
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Rongzhang Chen
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tian Li
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinli Gao
- Department of Pathology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xia Gu
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xuyou Zhu
- Department of Pathology, Tongji Hospital Affiliated to Tongji University, Shanghai, China
| | - Lianfeng Jin
- Department of Scientific Affairs, Vision Medical Center for Infectious Diseases, Guangdong, China
| | - Yi Shi
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Clinical School of Nanjing, Nanjing, China
| | - Qiang Li
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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Abstract
PURPOSE OF REVIEW The coronavirus disease 2019 pandemic demonstrated broad utility of pathogen sequencing with rapid methodological progress alongside global distribution of sequencing infrastructure. This review considers implications for now moving clinical metagenomics into routine service, with respiratory metagenomics as the exemplar use-case. RECENT FINDINGS Respiratory metagenomic workflows have completed proof-of-concept, providing organism identification and many genotypic antimicrobial resistance determinants from clinical samples in <6 h. This enables rapid escalation or de-escalation of empiric therapy for patient benefit and reducing selection of antimicrobial resistance, with genomic-typing available in the same time-frame. Attention is now focussed on demonstrating clinical, health-economic, accreditation, and regulatory requirements. More fundamentally, pathogen sequencing challenges the traditional culture-orientated time frame of microbiology laboratories, which through automation and centralisation risks becoming increasingly separated from the clinical setting. It presents an alternative future where infection experts are brought together around a single genetic output in an acute timeframe, aligning the microbiology target operating model with the wider human genomic and digital strategy. SUMMARY Pathogen sequencing is a transformational proposition for microbiology laboratories and their infectious diseases, infection control, and public health partners. Healthcare systems that link output from routine clinical metagenomic sequencing, with pandemic and antimicrobial resistance surveillance, will create valuable tools for protecting their population against future infectious diseases threats.
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Affiliation(s)
- Jonathan D Edgeworth
- Department of Infectious Diseases, Guy's & St Thomas' NHS Foundation Trust & Department of Infectious Diseases, Kings College London, UK
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Lin T, Tu X, Zhao J, Huang L, Dai X, Chen X, Xu Y, Li W, Wang Y, Lou J, Wu S, Zhang H. Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia. Front Cell Infect Microbiol 2023; 13:1136588. [PMID: 37009509 PMCID: PMC10061305 DOI: 10.3389/fcimb.2023.1136588] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
Background Community-acquired pneumonia (CAP) is an extraordinarily heterogeneous illness, both in the range of responsible pathogens and the host response. Metagenomic next-generation sequencing (mNGS) is a promising technology for pathogen detection. However, the clinical application of mNGS for pathogen detection remains challenging. Methods A total of 205 patients with CAP admitted to the intensive care unit were recruited, and broncho alveolar lavage fluids (BALFs) from 83 patients, sputum samples from 33 cases, and blood from 89 cases were collected for pathogen detection by mNGS. At the same time, multiple samples of each patient were tested by culture. The diagnostic performance was compared between mNGS and culture for pathogen detection. Results The positive rate of pathogen detection by mNGS in BALF and sputum samples was 89.2% and 97.0%, which was significantly higher (P < 0.001) than that (67.4%) of blood samples. The positive rate of mNGS was significantly higher than that of culture (81.0% vs. 56.1%, P = 1.052e-07). A group of pathogens including Mycobacterium abscessus, Chlamydia psittaci, Pneumocystis jirovecii, Orientia tsutsugamushi, and all viruses were only detected by mNGS. Based on mNGS results, Escherichia coli was the most common pathogen (15/61, 24.59%) of non-severe patients with CAP, and Mycobacterium tuberculosis was the most common pathogen (21/144, 14.58%) leading to severe pneumonia. Pneumocystis jirovecii was the most common pathogen (26.09%) in severe CAP patients with an immunocompromised status, which was all detected by mNGS only. Conclusion mNGS has higher overall sensitivity for pathogen detection than culture, BALF, and sputum mNGS are more sensitive than blood mNGS. mNGS is a necessary supplement of conventional microbiological tests for the pathogen detection of pulmonary infection.
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Affiliation(s)
- Tianlai Lin
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Xueliang Tu
- Department of Clinical Laboratory, Huanghe Sanmenxia Hospital Affiliated to Henan University of Science and Technology, Sanmenxia, China
| | - Jiangman Zhao
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Ling Huang
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Xiaodong Dai
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Xiaoling Chen
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Yue Xu
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Wushuang Li
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Yaoyao Wang
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Jingwei Lou
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Shouxin Wu
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
| | - Hongling Zhang
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
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Huang L, Xu S, Huang Z, Chen Y, Xu N, Xie B. Risk factors associated with Pneumocystis jirovecii pneumonia in non-HIV immunocompromised patients and co-pathogens analysis by metagenomic next-generation sequencing. BMC Pulm Med 2023; 23:72. [PMID: 36829171 PMCID: PMC9951498 DOI: 10.1186/s12890-022-02300-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/26/2022] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Pneumocystis jirovecii pneumonia (PJP) is one of the most common opportunistic infections in immunocompromised patients. However, the accurate prediction of the development of PJP in non-HIV immunocompromised patients is still unclear. METHODS Non-HIV immunocompromised patients confirmed diagnosis of PJP by the clinical symptoms, chest computed tomography and etiological results of metagenomic next-generation sequencing (mNGS) were enrolled as observation group. Another group of matched non-HIV immunocompromised patients with non-PJP pneumonia were enrolled to control group. The risk factors for the development of PJP and the co-pathogens in the bronchoalveolar lavage fluid (BALF) detected by mNGS were analyzed. RESULTS: A total of 67 (33 PJP, 34 non-PJP) participants were enrolled from Fujian Provincial Hospital. The ages, males and underlying illnesses were not significantly different between the two groups. Compared to non-PJP patients, PJP patients were more tends to have the symptoms of fever and dyspnea. The LYM and ALB were significantly lower in PJP patients than in non-PJP patients. Conversely, LDH and serum BDG in PJP patients were significantly higher than in non-PJP controls. For immunological indicators, the levels of immunoglobulin A, G, M and complement C3, C4, the numbers of T, B, and NK cells, had no statistical difference between these two groups. Logistic multivariate analysis showed that concomitant use of corticosteroids and immunosuppressant (OR 14.146, P = 0.004) and the lymphocyte counts < 0.7 × 109/L (OR 6.882, P = 0.011) were risk factors for the development of PJP in non-HIV immunocompromised patients. 81.82% (27/33) and 64.71% (22/34) mixed infections were identified by mNGS in the PJP group and non-PJP group separately. CMV, EBV and Candida were the leading co-pathogens in PJP patients. The percentages of CMV and EBV identified by mNGS in PJP group were significantly higher than those in the control group(p < 0.005). CONCLUSIONS: Clinicians should pay close attention to the development of PJP in non-HIV immunocompromised patients who possess the risk factors of concomitant use of corticosteroids and immunosuppressant and the lymphocyte counts < 0.7 × 109/L. Prophylaxis for PJP cannot rely solely on CD4+ T counts in non-HIV immunocompromised patients. Whether CMV infection increases the risk of PJP remains to be further investigated.
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Affiliation(s)
- Liping Huang
- grid.256112.30000 0004 1797 9307Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001 Fujian Province China ,grid.415108.90000 0004 1757 9178Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, 350001 Fujian Province China
| | - Shuyun Xu
- grid.256112.30000 0004 1797 9307Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001 Fujian Province China
| | - Zhimin Huang
- grid.256112.30000 0004 1797 9307Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001 Fujian Province China
| | - Yusheng Chen
- grid.256112.30000 0004 1797 9307Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001 Fujian Province China ,grid.415108.90000 0004 1757 9178Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, 350001 Fujian Province China
| | - Nengluan Xu
- grid.256112.30000 0004 1797 9307Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001 Fujian Province China ,grid.415108.90000 0004 1757 9178Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, 350001 Fujian Province China
| | - Baosong Xie
- Shengli Clinical Medical college of Fujian Medical University, Fuzhou, 350001, Fujian Province, China. .,Department of Respiratory and Critical Care Medicine, Fujian Provincial Hospital, Fuzhou, 350001, Fujian Province, China.
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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: 1.5] [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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Diagnostic Value of Metagenomic Next-Generation Sequencing for Pneumonia in Immunocompromised Patients. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:5884568. [PMID: 36507192 PMCID: PMC9731749 DOI: 10.1155/2022/5884568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Introduction The diagnosis of pulmonary infection and the identification of pathogens are still clinical challenges in immunocompromised patients. Metagenomic next-generation sequencing (mNGS) has emerged as a promising infection diagnostic technique. However, its diagnostic value in immunocompromised patients needs further exploration. Purposes This study was to evaluate the diagnostic value of mNGS compared with comprehensive conventional pathogen tests (CTs) in the etiology of pneumonia in immunocompromised patients and immunocompetent patients. Methods We retrospectively reviewed 53 patients who were diagnosed with pneumonia from May 2019 to June 2021. There were 32 immunocompromised patients and 21 immunocompetent patients with pneumonia who received both mNGS and CTs. The diagnostic performance was compared between mNGS and CTs in immunocompromised patients, using the composite diagnosis as the reference standard. And, the diagnostic value of mNGS for mixed infections was further analyzed. Results Compared to immunocompetent patients, the most commonly pathogens, followed by Cytomegalovirus, Pneumocystis jirovecii and Klebsiella pneumoniae in immunocompromised patients. Furthermore, more mixed infections were diagnosed, and bacterial-fungal-virus coinfection was the most frequent combination (43.8%). mNGS can detect more types of pathogenic microorganisms than CTs in both groups (78.1% vs. 62.5%, P = 0.016and 57.1% vs. 42.9%, P = 0.048). The overall diagnostic positive rate of mNGS for pathogens was higher in immunocompromised patients (P = 0.002). In immunocompromised patients, a comparable diagnostic accuracy of mNGS and CTs was found for bacterial, fungal, and viral infections and coinfection. mNGS had a much higher sensitivity for bacterial infections (92.9% vs. 50%, P < 0.001) and coinfections (68.8% vs. 48.3%, P < 0.05), and it had no significant advantage in the detection of fungal infections, mainly due to the high sensitivity for Pneumocystis jirovecii in both groups. Conclusion mNGS is more valuable in immunocompromised patients and exhibits apparent advantages in detecting bacterial and mixed infections. It may be an alternative or complementary diagnostic method for the diagnosis of complicated infections in immunocompromised patients.
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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: 26] [Impact Index Per Article: 8.7] [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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Zhang J, Gao L, Zhu C, Jin J, Song C, Dong H, Li Z, Wang Z, Chen Y, Yang Z, Tan Y, Wang L. Clinical value of metagenomic next-generation sequencing by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid in suspected community-acquired pneumonia patients. Front Cell Infect Microbiol 2022; 12:1021320. [PMID: 36237436 PMCID: PMC9551279 DOI: 10.3389/fcimb.2022.1021320] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
At present, metagenomic next-generation sequencing (mNGS) based on Illumina platform has been widely reported for pathogen detection. There are few studies on the diagnosis of major pathogens and treatment regulation using mNGS based on Illumina versus Nanopore. We aim to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid (BALF) in suspected community-acquired pneumonia (CAP) patients. BALF samples collected from 66 suspected CAP patients within 48 hours of hospitalization were divided into two parts, one for conventional culture and the other for mNGS by two platforms (Illumina and Nanopore). The clinical value based on infection diagnosis, diagnostic performance for main pathogens and treatment guidance were assessed. More types of species were detected by Nanopore than Illumina, especially in viruses, fungus and mycobacterium. Illumina and Nanopore showed similar detectability in bacterium except for mycobacterium tuberculosis complex/nontuberculosis mycobacteria. Pathogenic infection was established or excluded in 53 of 66 patients. There was little difference in the coincidence rate between Illumina and Nanopore with the clinical diagnosis, but both were superior to the culture (57.81%, 59.38%, 25%, respectively). Compared with Illumina, the diagnostic area under the curve of Nanopore was higher in fungi, but lower in bacteria and Chlamydia psittaci. There was no statistically significant difference between Illumina and Nanopore in guiding drug treatment (56.1% vs. 50%, p=0.43), but both were superior to the culture (56.1% vs. 28.8%, p=0.01; 50% vs. 28.8%, p=0.01). Single inflammatory indicators could not be used to determine whether the patients with culture-negative BALF were established or excluded from infection. The species detected at 1 h and 4 h by Nanopore were consistent to some extent, and its turn-around time (TAT) was significantly shorter than Illumina (p<0.01). Illumina and Nanopore both have its own advantages in pathogenic diagnosis and play similar roles in infection diagnosis and guiding clinical treatment. Nanopore has a relatively short TAT, which may be promising in rapid etiological diagnosis of acute and critically ill patients.
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Affiliation(s)
- Jing Zhang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Lin Gao
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Chi Zhu
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Jiajia Jin
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Hang Dong
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Zhenzhong Li
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, China
| | - Zheng Wang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yubao Chen
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zhenhua Yang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yan Tan
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Li Wang
- Department of Respiratory and Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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Zhang Y, Zeng Z, Li F, Peng Z, Xia H, Zeng Y, Chen H, Wang Y, Xie W, Zhang Y, Tang Z. Metagenomic next-generation sequencing in diagnosing Pneumocystis jirovecii pneumonia: A case report. Open Life Sci 2022; 17:938-943. [PMID: 36060643 PMCID: PMC9386609 DOI: 10.1515/biol-2022-0094] [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: 02/23/2022] [Revised: 04/28/2022] [Accepted: 05/18/2022] [Indexed: 11/15/2022] Open
Abstract
It remains a huge challenge for clinicians to diagnose Pneumocystis jirovecii pneumonia (PJP) by a conventional method, which leads to delay in diagnosing PJP, accounting for higher mortality in patients with rheumatoid arthritis (RA). A 69-year-old woman, who suffered from RA for years, developed acute respiratory failure. The computed tomography scan showed diffused effusion and ground glass opacity in both lungs, which could not be differentiated from interstitial pneumonia. Metagenomic next-generation sequencing (mNGS) revealed P. jirovecii in both serum and bronchoalveolar lavage fluid with reads per million (RPM) of 17 and 437, while other diagnostic tests did not detect any pathogenic microorganism. The results were verified by quantitative polymerase chain reaction (mtSSU region) against the same samples. The DNA RPM of P. jirovecii declined notably after treatment with trimethoprim/sulfamethoxazole. The patient was discharged without treatment and finally passed away. This case fully highlights the sensitivity of mNGS in early diagnosis of PJP, which is of great significance for prognosis and treatment. Nonetheless, the clinical application of mNGS is worth further standardization and normalization.
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Affiliation(s)
- Yuan Zhang
- Department of Intensive Care Unit, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan 528200, China
| | - Zhaoshang Zeng
- Department of Intensive Care Unit, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan 528200, China
| | - Fenghui Li
- Department of Intensive Care Unit, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan 528200, China
| | - Zhiyun Peng
- Department of Intensive Care Unit, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan 528200, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd, Beijing 100176, China
| | - Yunyi Zeng
- Department of Intensive Care Unit, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan 528200, China
| | - Haimin Chen
- Department of Intensive Care Unit, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan 528200, China
| | - Yingjing Wang
- Department of Intensive Care Unit, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan 528200, China
| | - Weining Xie
- Department of Infectious Disease, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan 528200, China
| | - Yanhua Zhang
- Department of Nutriology, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan 528200, China
| | - Zhongxiang Tang
- Department of Intensive Care Unit, Guangdong Provincial Hospital of Integrated Traditional Chinese and Western Medicine, Foshan 528200, China
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Zhang Y, Wang W, Zhang Y, Zhai S, Xia H, Zhang X. Pulmonary Cryptococcosis Diagnosed by Metagenomic Next-Generation Sequencing in a Young Patient With Normal Immune Function: A Case Report. Front Public Health 2022; 10:942282. [PMID: 35937275 PMCID: PMC9353032 DOI: 10.3389/fpubh.2022.942282] [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: 05/12/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022] Open
Abstract
Background Pulmonary cryptococcosis (PC) is a serious opportunistic fungal infection that usually occurs in immunocompromised patients. This disease is often difficult to diagnose in time due to its clinical manifestations and radiological feature similar to other pulmonary infections, as well as the low sensitivity of conventional diagnostic methods. Cryptococcosis in immune-competent patients is rare. Case Presentation Here we report a case of PC in an immune-competent patient. Tuberculosis was suspected according to radiological features due to the positive T-lymphocyte spot test and pure protein derivative skin test. To further detect the pathogen, bronchoalveolar lavage fluid (BALF) was collected for metagenomic next-generation sequencing (mNGS). Cryptococcus neoformans (one specific read) was identified by mNGS, indicating the PC of this patient. The following BALF culture and cryptococcal antigen lateral flow assay (CrAg-LFA) test also showed Cryptococcus infection, confirming the mNGS detection. Voriconazole (0.4 g daily) was given orally according to the subsequent susceptibility results. After seven months of treatment, the patient's condition improved. Conclusion Metagenomic next-generation sequencing (mNGS) is a better diagnostic tool to help clinicians distinguish pulmonary cryptococcosis from other atypical pulmonary infections.
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Affiliation(s)
- Yingyu Zhang
- Department of Tuberculosis, Foshan Fourth People's Hospital, Foshan, China
| | - Weiliang Wang
- Department of Tuberculosis, Foshan Fourth People's Hospital, Foshan, China
| | - Yingxuan Zhang
- Department of Tuberculosis, Foshan Fourth People's Hospital, Foshan, China
| | - Sina Zhai
- Department of Tuberculosis, Foshan Fourth People's Hospital, Foshan, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech, Beijing, China
| | - Xilin Zhang
- Department of Tuberculosis, Foshan Fourth People's Hospital, Foshan, China
- *Correspondence: Xilin Zhang
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