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Liu M, Zhang H, Li L, Mao J, Li R, Yin J, Wu X. The etiological diagnostic value of metagenomic next-generation sequencing in suspected community-acquired pneumonia. BMC Infect Dis 2024; 24:626. [PMID: 38914949 PMCID: PMC11194883 DOI: 10.1186/s12879-024-09507-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/13/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND The emergence of metagenomic next-generation sequencing (mNGS) may provide a promising tool for early and comprehensive identification of the causative pathogen in community-acquired pneumonia (CAP). In this study, we aim to further evaluate the etiological diagnostic value of mNGS in suspected CAP. METHODS A total of 555 bronchoalveolar lavage fluid (BALF) samples were collected for pathogen detection by mNGS from 541 patients with suspected CAP. The clinical value was assessed based on infection diagnosis and treatment guidance. The diagnostic performance for pathogen identification by mNGS and sputum culture and for tuberculosis (TB) by mNGS and X-pert MTB/RIF were compared. To evaluate the potential for treatment guidance, we analyzed the treatment regimen of patients with suspected CAP, including imaging changes of lung after empirical antibacterial therapy, intensified regimen, antifungal treatment, and a 1-year follow up for patients with unconfirmed diagnosis and non-improvement imaging after anti-infective treatment and patients with high suspicion of TB or NTM infection who were transferred to the Wuhan Pulmonary Hospital for further diagnosis and even anti-mycobacterium therapy. RESULTS Of the 516 BALF samples that were analyzed by both mNGS and sputum culture, the positivity rate of mNGS was significantly higher than that of sputum culture (79.1% vs. 11.4%, P = 0.001). A total of 48 samples from patients with confirmed TB were analyzed by both mNGS and X-pert MTB/RIF, and the sensitivity of mNGS for the diagnosis of active TB was significantly lower than that of X-pert MTB/RIF (64.6% vs. 85.4%, P = 0.031). Of the 106 pathogen-negative cases, 48 were ultimately considered non-infectious diseases, with a negative predictive value of 45.3%. Of the 381 pathogen-positive cases, 311 were eventually diagnosed as CAP, with a positive predictive value of 81.6%. A total of 487 patients were included in the evaluation of the therapeutic effect, and 67.1% improved with initial empirical antibiotic treatment. Of the 163 patients in which bacteria were detected, 77.9% improved with antibacterial therapy; of the 85 patients in which fungi were detected, 12.9% achieved remission after antifungal therapy. CONCLUSIONS Overall, mNGS had unique advantages in the detection of suspected CAP pathogens. However, mNGS was not superior to X-pert MTB/RIF for the diagnosis of TB. In addition, mNGS was not necessary as a routine test for all patients admitted with suspected CAP. Furthermore, when fungi are detected by mNGS, antifungal therapy should be cautious.
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Affiliation(s)
- Mengling Liu
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haiyue Zhang
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Liangyu Li
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jieyu Mao
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ruiyun Li
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jing Yin
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaojun Wu
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
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Liu L, Ji T, Chen R, Fan L, Dai J, Qiu Y. High prevalence of pneumocystis pneumonia in interstitial lung disease: a retrospective study. Infection 2024; 52:985-993. [PMID: 38147199 DOI: 10.1007/s15010-023-02148-y] [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: 07/09/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Interstitial lung disease (ILD) is a new risk category for pneumocystis pneumonia (PCP) with a high mortality rate. The definite diagnostic criteria of PCP in ILD patients have not been established until now. The aims of this study were to identify potential risk factors of PCP in patients with ILD, and to evaluate the performance of metagenomic next-generation sequencing (mNGS), CD4 + T cell count, (1-3)-β-D-Glucan (BG) and lactate dehydrogenase (LDH) in the diagnosis of PCP in ILD patients. METHODS This is a retrospective, single-center, case-control study. ILD patients who underwent mNGS from December 2018 to December 2022 were included in the study. Based on the diagnosis criteria of PCP, these patients were divided into PCP-ILD and non-PCP-ILD groups. The potential risk factors for PCP occurrence in ILD patients were analysed via logistic regression. The diagnostic efficacy of mNGS was compared with serological biomarkers. RESULTS 92 patients with ILD were enrolled, 31 of which had a definite PCP and were assigned to the PCP-ILD group while 61 were to the non-PCP-ILD group. The infection rate of PJ in ILD patients was 33.7% (31/92). The history of glucocorticoid therapy, CD4 + T cell count, BG level and traction bronchiectasis on HRCT were associated with PCP occurrence in ILD patients. LDH level did not reach statistical significance in the logistic regression analysis. mNGS was confirmed as the most accurate test for PCP diagnosis in ILD patients. CONCLUSION ILD is a new risk group of PCP with high PCP prevalence. Clinicians should pay close attention to the occurrence of PCP in ILD patients who possess the risk factors of previous glucocorticoid therapy, decreased CD4 + T cell count, increased BG level and absence of traction bronchiectasis on HRCT. mNGS showed the most excellent performance for PCP diagnosis in ILD patients. Peripheral blood CD4 + T cell count and BG level are alternative diagnostic methods for PCP in ILD patients. However, the diagnostic value of serum LDH level was limited in ILD patients.
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Affiliation(s)
- Ling Liu
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China
| | - Tong Ji
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China
| | - Ranxun Chen
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China
| | - Li Fan
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China
| | - Jinghong Dai
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China.
| | - Yuying Qiu
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China.
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Saadatzadeh T, Angarone M, Stosor V. Pneumocystis jirovecii in solid organ transplant recipients: updates in epidemiology, diagnosis, treatment, and prevention. Curr Opin Infect Dis 2024; 37:121-128. [PMID: 38230604 DOI: 10.1097/qco.0000000000001002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
PURPOSE OF REVIEW This review highlights the epidemiology of Pneumocystis jirovecii pneumonia in solid organ transplant recipients, advancements in the diagnostic landscape, and updates in treatment and prevention. RECENT FINDINGS The increasing use of immune-depleting agents in the context of solid organ transplantation has given rise to P. jirovecii pneumonia in this population. The use of prophylaxis has dramatically reduced risk of infection; however, late-onset infections occur after cessation of prophylaxis and in the setting of lymphopenia, advancing patient age, acute allograft rejection, and cytomegalovirus infection. Diagnosis requires respiratory specimens, with PCR detection of Pneumocystis replacing traditional staining methods. Quantitative PCR may be a useful adjunct to differentiate between infection and colonization. Metagenomic next-generation sequencing is gaining attention as a noninvasive diagnostic tool. Trimethoprim-sulfamethoxazole remains the drug of choice for treatment and prevention of Pneumocystis pneumonia. Novel antifungal agents are under investigation. SUMMARY P. jirovecii is a fungal opportunistic pathogen that remains a cause of significant morbidity and mortality in solid organ transplant recipients. Early detection and timely treatment remain the pillars of management.
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Affiliation(s)
| | | | - Valentina Stosor
- Divisions of Infectious Diseases
- Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Huang MQ, Zheng TT, Wang XR, Xiang F. The Clinical Value of Metagenomic Next-Generation Sequencing in Pneumocystis jirovecii Pneumonia. Infect Drug Resist 2024; 17:69-80. [PMID: 38223562 PMCID: PMC10787560 DOI: 10.2147/idr.s444571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/22/2023] [Indexed: 01/16/2024] Open
Abstract
Background The incidence of Pneumocystis jirovecii pneumonia (PJP) is increasing. Methods 108 patients were analysed retrospectively at the Wuhan Union Hospital. The patients were classified into the PJP group or the P. jirovecii colonisation (PJC) group based on clinical diagnosis. Clinical data included demographics, laboratory examinations, treatment, and outcomes. Results A notable difference in the fungal load was seen between two groups, with median reads of 3215.79 vs. 5.61 in two groups, respectively (P<0.001). The optimal threshold value for discriminating P. jirovecii infection between colonisation for mNGS was six, and serum (1,3)-β-D-glucan (BDG) was 47.6 pg/mL. Besides, the positive detection rate of mNGS for co-pathogens in PJP patients was significantly higher than that of culture (88.16% vs. 22.37%, P<0.0001). Epstein-Barr virus and cytomegalovirus were the most common pathogens of co-infection in PJP patients. The antibiotic therapy in PJP patients was adjusted according to the mNGS results, of which seventeen (22.37%) were downgraded, 38 (50.0%) patients were upgraded, and 21 (27.63%) were unchanged. And almost all patients showed significant improvement in C-reactive protein. Conclusion mNGS is a promising and valuable technique with good performance for differentiating P. jirovecii infection and colonisation, the detection of pathogens, and antibiotic treatment.
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Affiliation(s)
- Meng-Qi Huang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, People’s Republic of China
| | - Ting-Ting Zheng
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, People’s Republic of China
| | - Xiao-Rong Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, People’s Republic of China
| | - Fei Xiang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, People’s Republic of China
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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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Chen H, Liang Y, Wang R, Wu Y, Zhang X, Huang H, Yu X, Hong M, Yang J, Liao K, Xu H, Liu M, Chen P, Chen Y. Metagenomic next-generation sequencing for the diagnosis of Pneumocystis jirovecii Pneumonia in critically pediatric patients. Ann Clin Microbiol Antimicrob 2023; 22:6. [PMID: 36647095 PMCID: PMC9841943 DOI: 10.1186/s12941-023-00555-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [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
- grid.412615.50000 0004 1803 6239Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Yujian Liang
- grid.412615.50000 0004 1803 6239Department of Pediatric Intensive Care Unit, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Ruizhi Wang
- grid.412615.50000 0004 1803 6239Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Yijie Wu
- grid.12981.330000 0001 2360 039XZhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China
| | - Xiaoyun Zhang
- grid.12981.330000 0001 2360 039XZhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China
| | - Hao Huang
- grid.412615.50000 0004 1803 6239Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Xuegao Yu
- grid.412615.50000 0004 1803 6239Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Mengzhi Hong
- grid.412615.50000 0004 1803 6239Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Juhua Yang
- grid.508230.cVision Medicals Co., Ltd, Guangzhou, China
| | - Kang Liao
- grid.412615.50000 0004 1803 6239Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Hongxu Xu
- grid.412615.50000 0004 1803 6239Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Min Liu
- grid.412615.50000 0004 1803 6239Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Peisong Chen
- grid.412615.50000 0004 1803 6239Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
| | - Yili Chen
- grid.412615.50000 0004 1803 6239Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
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Zhao M, Yue R, Wu X, Gao Z, He M, Pan L. The diagnostic value of metagenomic next-generation sequencing for identifying Pneumocystis jirovecii infection in non-HIV immunocompromised patients. Front Cell Infect Microbiol 2022; 12:1026739. [PMID: 36389151 PMCID: PMC9647189 DOI: 10.3389/fcimb.2022.1026739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background Pneumocystis jirovecii pneumonia (PJP) remains an important cause of morbidity and mortality in non-HIV immunocompromised patients especially in transplant recipients. But its diagnosis remains challenging due to the insuffificient performance of conventional methods for diagnosing Pneumocystis jirovecii(P. jirovecii) infection. Therefore, the auxiliary diagnostic function of metagenomics next-generation sequencing (mNGS) in clinical practice is worth of exploring. Method 34 non-HIV immunocompromised patients who were diagnosed as PJP by clinical manifestations, imaging findings, immune status of the host, and Methenamine silver staining were tested by mNGS from October 2018 to December 2020 in Sichuan Provincial People’s Hospital. The clinical performances of mNGS for P. jirovecii infection diagnosis were also evaluated with genome reads abundance and comparing with other traditional diagnostic methods. Results We diagnosed a total of 34 non-HIV PJP patients by the clinical composite diagnosis. Our data shows that, compared with the clinical microbiological test, the detection rate of mNGS for P. jirovecii in non-HIV infected PJP patients is significantly higher than that of Methenamine silver staining and serum 1-3-β-D-glucan. mNGS can be used as an auxiliary diagnostic tool to help diagnosis. The number of reads mapped to the genome of P. jirovecii and the duration of patients from onset to sampling collection were statistically significant between the two groups (Reads>100 and Reads ≤ 100) (8days vs. 23days, p=0.020). In addition, univariate analysis showed that C-reactive protein (15.8mg/L vs.79.56mg/L, p=0.016), lactate dehydrogenase (696U/l vs. 494U/l, p=0.030) and procalcitonin (0.09ng/ml vs. 0.59ng/ml, p=0.028) was also statistically significant between the two groups. Conclusions An effective detection rate was achieved in PJP patients using mNGS testing of bronchoalveolar lavage fluid (BALF) or blood. The study also confirmed that the abundance of reads of P. jirovecii is related to the interval between the onset and sample collection. And the inflammation status during simultaneous mNGS detection might determine the abundance of pathogens. Hence, we conclude that the mNGS strategy could benefit disease diagnosis as well as treatment when complicated clinical infections appeared.
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Affiliation(s)
- Mengyi Zhao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Ruiming Yue
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Xiaoxiao Wu
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Zhan Gao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Miao He
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
- *Correspondence: Miao He, ; Lingai Pan,
| | - Lingai Pan
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- *Correspondence: Miao He, ; Lingai Pan,
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Hou JN, Liu HD, Tan QY, Cao FA, Wang SL, Yao MY, Zhao YC. Risk factors of in-hospital mortality in patients with pneumocystis pneumonia diagnosed by metagenomics next-generation sequencing. Front Cell Infect Microbiol 2022; 12:994175. [PMID: 36225233 PMCID: PMC9549864 DOI: 10.3389/fcimb.2022.994175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives The metagenomic next-generation sequencing (mNGS) test is useful for rapid and accurate detection and identification of pathogenic microorganisms. The aim of the present study was to investigate the factors associated with in-hospital mortality in pneumocystis pneumonia (PCP) patients with mNGS-assisted diagnosis. Methods Our study enrolled 154 patients with mNGS-positive PCP from August 2018 to February 2022 at the First Affiliated Hospital of Zhengzhou University respectively. Patients were divided into the survivor group (n=98) and the death group (n=56) according to whether in-hospital death occurred. Baseline characteristics, patients’ pre-hospital symptoms and patients’ CT imaging performance during hospitalization were carefully compared between the two groups. Risk factors for the occurrence of in-hospital death were sought by selecting indicators that were significantly different between the two groups for modelling and performing multiple logistic regression analysis. Results Compared with the in-hospital death patients, the survivors were younger and had higher levels of albumin (ALB) (age: 50.29 ± 14.63 years vs 59.39 ± 12.27 years, p<0.001; ALB: 32.24 ± 5.62 g/L vs 29.34 ± 5.42g/L, p=0.002; respectively), while the levels of lactate dehydrogenase (LDH) and C-reactive protein CRP were lower (LDH: 574.67 ± 421.24 U/L vs 960.80 ± 714.94 U/L, p=0.001; CRP: 54.97 ± 55.92 mg/L vs80.45 ± 73.26 mg/L, p=0.018; respectively). Multiple logistic regression analysis revealed that age, the baseline LDH and CRP levels were all positively associated with high in-hospital mortality [age: OR(95%CI): 1.115 (1.062-1.172), p<0.001; LDH: OR(95%CI): 1.002 (1.001-1.003), p<0.001; CRP: OR(95%CI): 1.008 (1.000-1.017), p=0.045; respectively] while the platelet counts was negatively associated with it [OR(95%CI): 0.986 (0.979-0.992), p<0.001]. Conclusions Old age, high baseline levels of LDH and CRP and low platelet counts were risk factors of the in-hospital mortality in mNGS positive PCP patients.
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Affiliation(s)
- Jun-Na Hou
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Heng-Dao Liu
- Department of Cardiology, Cardiovascular Center, Henan Key Laboratory of Hereditary Cardiovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiu-Yue Tan
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng-An Cao
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shi-Lei Wang
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Meng-Ying Yao
- Department of Pulmonary, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Meng-Ying Yao, ; Yang-Chao Zhao,
| | - Yang-Chao Zhao
- Department of Extracorporeal Life Support Center, Department of Cardiac Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Meng-Ying Yao, ; Yang-Chao Zhao,
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Liu L, Yuan M, Sun S, Wang J, Shi Y, Yu Y, Su X. The Performance of Metagenomic Next-Generation Sequence in the Diagnosis of Suspected Opportunistic Infections in Patients with Acquired Immunodeficiency Syndrome. Infect Drug Resist 2022; 15:5645-5653. [PMID: 36187731 PMCID: PMC9518679 DOI: 10.2147/idr.s378249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
Abstract
Background For acquired immunodeficiency syndrome (AIDS) patients with suspected opportunistic infections, the rapid and accurate identification of pathogens remains a challenge. Metagenomic next-generation sequencing (mNGS) has emerged as a pan-pathogen assay for infectious diseases diagnosis, but its guiding significance for diagnosis and antimicrobials treatment in AIDS patients with suspected opportunistic infections is still not well established. In this study, we compared the microbiological diagnostic value of mNGS with that of conventional microbiological tests (CMTs) in AIDS patients with suspected opportunistic infections. Methods From January 2018 to February 2021, a retrospective study was performed at four tertiary teaching hospitals in China and data of 86 AIDS patients with suspected opportunistic infections were collected. The pathogen detection performance of mNGS and CMTs were compared. Results Positive agreement between mNGS and clinical diagnosis was significantly higher than that of CMTs (65/86 (75.6%) vs 37/86 (43.0%)). In addition, mNGS identified more bacterial (25 vs 2), fungal (5 vs 3), viral (9 vs 2) organisms compared with CMTs. Mixed infection were detected in 34 patients by mNGS combined with CMTs. Viruses (94.1%, 32/34) and fungi (94.1%, 32/34) were commonly seen in the mixed infection cases. mNGS helped identify the pathogen or guide appropriate treatment in 49/86 (57%) patients. Meanwhile, CMTs also contributed in the decision of appropriate treatment in 28 patients. The successful de-escalation or discontinuation of treatment was supported in 37 patients with the help of mNGS. We observed a significant reduction in the number of patients being prescribed foscarnet (52.3% vs 23.26%, p < 0.001), moxifloxacin (34.9% vs 10.5%, p = 0.005), and levofloxacin (32.6% vs 14%, p = 0.001) before and after mNGS. Conclusion For AIDS patients with suspected opportunistic infections, mNGS can provide early, noninvasive, and rapid microbiological diagnosis. mNGS may lead to a more precise antimicrobial treatment and reduced the unreasonable use of antimicrobials.
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Affiliation(s)
- Li Liu
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, People’s Republic of China
- Department of Infectious Disease, Hunan Provincial People’s Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, Hunan Province, People’s Republic of China
| | - Mingjuan Yuan
- Department of Infectious Disease, The Central Hospital of Yueyang, Yueyang, Hunan Province, People’s Republic of China
| | - Siqing Sun
- Department of General Medicine, The Second Hospital of Nanjing, Nanjing Hospital of Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Jinrong Wang
- Department of Respiratory and Critical Care Medicine, Hengshui People’s hospital, Hengshui, Hebei Province, People’s Republic of China
| | - Yi Shi
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, People’s Republic of China
| | - Yamin Yu
- Department of Nephrology, Ningxiang People’s Hospital, Changsha, Hunan Province, People’s Republic of China
| | - Xin Su
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, People’s Republic of China
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Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: a Multicenter Retrospective Study. Microbiol Spectr 2022; 10:e0247321. [PMID: 35943274 PMCID: PMC9431624 DOI: 10.1128/spectrum.02473-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has been gradually applied to clinical practice due to its unbiased characteristics of pathogen detection. However, its diagnostic performance and clinical value in suspected pulmonary infection need to be evaluated. We systematically reviewed the clinical data of 246 patients with suspected pulmonary infection from 4 medical institutions between January 2019 and September 2021. The diagnostic performances of mNGS and conventional testing (CT) were systematically analyzed based on bronchoalveolar lavage fluid (BALF). The impacts of mNGS and CT on diagnosis modification and treatment adjustment were also assessed. The positive rates of mNGS and CT were 47.97% and 23.17%, respectively. The sensitivity of mNGS was significantly higher than that of CT (53.49% versus 23.26%, P < 0.01), especially for infections of Mycobacterium tuberculosis (67.86% versus 17.86%, P < 0.01), atypical pathogens (100.00% versus 7.14%, P < 0.01), viruses (92.31% versus 7.69%, P < 0.01), and fungi (78.57% versus 39.29%, P < 0.01). The specificity of mNGS was superior to that of CT, with no statistical difference (90.32% versus 77.42%, P = 0.167). The positive predictive value (PPV) and negative predictive value (NPV) of mNGS were 97.46% and 21.88%, respectively. Diagnosis modification and treatment adjustment were conducted in 32 (32/246, 13.01%) and 23 (23/246, 9.35%) cases, respectively, according to mNGS results only. mNGS significantly improved the diagnosis of suspected pulmonary infection, especially infections of M.tuberculosis, atypical pathogens, viruses, and fungi, and it demonstrated the pathogen distribution of pulmonary infections. It is expected to be a promising microbiological detection and diagnostic method in clinical practice. IMPORTANCE Pulmonary infection is a heterogeneous and complex infectious disease with high morbidity and mortality worldwide. In clinical practice, a considerable proportion of the etiology of pulmonary infection is unclear, microbiological diagnosis being challenging. Metagenomic next-generation sequencing detects all nucleic acids in a sample in an unbiased manner, revealing the microbial community environment and organisms and improving the microbiological detection and diagnosis of infectious diseases in clinical settings. This study is the first multicenter, large-scale retrospective study based entirely on BALF for pathogen detection by mNGS, and it demonstrated the superior performance of mNGS for microbiological detection and diagnosis of suspected pulmonary infection, especially in infections of Mycobacterium tuberculosis, atypical pathogens, viruses, and fungi. It also demonstrated the pathogen distribution of pulmonary infections in the real world, guiding targeted treatment and improving clinical management and prognoses.
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Sun L, Zhang S, Yang Z, Yang F, Wang Z, Li H, Li Y, Sun T. Clinical Application and Influencing Factor Analysis of Metagenomic Next-Generation Sequencing (mNGS) in ICU Patients With Sepsis. Front Cell Infect Microbiol 2022; 12:905132. [PMID: 35909965 PMCID: PMC9326263 DOI: 10.3389/fcimb.2022.905132] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
Objective To analyze the clinical application and related influencing factors of metagenomic next-generation sequencing (mNGS) in patients with sepsis in intensive care unit (ICU). Methods The study included 124 patients with severe sepsis admitted to the ICU in the First Affiliated Hospital of Zhengzhou University from June 2020 to September 2021. Two experienced clinicians took blood mNGS and routine blood cultures of patients meeting the sepsis diagnostic criteria within 24 hours after sepsis was considered, and collection the general clinical data. Results mNGS positive rate was higher than traditional blood culture (67.74% vs. 19.35%). APACHE II score [odds ratio (OR)=1.096], immune-related diseases (OR=6.544), and hypertension (OR=2.819) were considered as positive independent factors for mNGS or culture-positive. The sequence number of microorganisms and pathogen detection (mNGS) type had no effect on prognosis. Age (OR=1.016), female (OR=5.963), myoglobin (OR=1.005), and positive virus result (OR=8.531) were independent risk factors of sepsis mortality. Adjusting antibiotics according to mNGS results, there was no statistical difference in the prognosis of patients with sepsis. Conclusion mNGS has the advantages of rapid and high positive rate in the detection of pathogens in patients with severe sepsis. Patients with high APACHE II score, immune-related diseases, and hypertension are more likely to obtain positive mNGS results. The effect of adjusting antibiotics according to mNGS results on the prognosis of sepsis needs to be further evaluated.
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Affiliation(s)
- Limin Sun
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuguang Zhang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ziyue Yang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fei Yang
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongqiang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yaoguang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tongwen Sun
- General Intensive Care Unit, Zhengzhou Key Laboratory of Sepsis, Henan Key Laboratory of Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Tongwen Sun,
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12
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Diagnostic value of metagenomic next-generation sequencing of bronchoalveolar lavage fluid for the diagnosis of suspected pneumonia in immunocompromised patients. BMC Infect Dis 2022; 22:416. [PMID: 35488253 PMCID: PMC9052728 DOI: 10.1186/s12879-022-07381-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/13/2022] [Indexed: 12/14/2022] Open
Abstract
Background To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in immunocompromised patients for the diagnosis of suspected pneumonia in comparison with that of conventional microbiological tests (CMTs). Methods Sixty-nine immunocompromised patients with suspected pneumonia received both CMTs and mNGS of BALF were analyzed retrospectively. The diagnostic value was compared between CMTs and mNGS, using the clinical composite diagnosis as the reference standard. Results Sixty patients were diagnosed of pneumonia including fifty-two patients with identified pathogens and eight patients with probable pathogens. Taking the composite reference standard as a gold standard, 42 pathogens were identified by CMTs including nine bacteria, 17 fungi, 8 virus, 6 Mycobacterium Tuberculosis, and two Legionella and 19(45%) of which were detected by BALF culture. As for mNGS, it identified 76 pathogens including 20 bacteria, 31 fungi, 14 virus, 5 Mycobacterium Tuberculosis, four Legionella and two Chlamydia psittaci. The overall detection rate of mNGS for pathogens were higher than that of CMTs. However, a comparable diagnostic accuracy of mNGS and CMTs were found for bacterial and viral infections. mNGS exhibited a higher diagnostic accuracy for fungal detection than CMTs (78% vs. 57%, P < 0.05), which mainly because of the high sensitivity of mNGS in patients with Pneumocystis jirovecii pneumonia (PJP) (100% vs. 28%, P < 0.05). Nineteen patients were identified as pulmonary co-infection, mNGS test showed a higher detection rate and broader spectrum for pathogen detection than that of CMTs in co-infection. Moreover, Pneumocystis jirovecii was the most common pathogen in co-infection and mNGS have identified much more co-pathogens of PJP than CMTs. Conclusions mNGS of BALF improved the microbial detection rate of pathogens and exhibited remarkable advantages in detecting PJP and identifying co-infection in immunocompromised patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07381-8.
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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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Duan J, Gao J, Liu Q, Sun M, Liu Y, Tan Y, Xing L. Characteristics and Prognostic Factors of Non-HIV Immunocompromised Patients With Pneumocystis Pneumonia Diagnosed by Metagenomics Next-Generation Sequencing. Front Med (Lausanne) 2022; 9:812698. [PMID: 35308503 PMCID: PMC8928194 DOI: 10.3389/fmed.2022.812698] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/20/2022] [Indexed: 11/27/2022] Open
Abstract
Objective The aim of this study was to evaluate the potential of metagenomic next-generation sequencing (mNGS) for the diagnosis of pneumocystis pneumonia (PCP) in patients with non-human immunodeficiency virus-infection and to discuss the clinical characteristics and identify prognostic factors associated with patients with non-HIV PCP. Methods Forty-six patients with PCP who were admitted in respiratory intensive care unit (ICU) between May 2018 and May 2020 were retrospectively reviewed. The subjects were divided into survivor and non-survivor groups according to the patients' outcome. Conventional methods and mNGS for detecting Pneumocystis jirovecii (P. jirovecii) were analyzed. The patients' demographics, comorbidities, laboratory parameters, and treatments were compared and evaluated in both groups to identify risk factors for mortality by using univariate and multivariate logistic regression. Results Metagenomic next-generation sequencing (mNGS) showed a satisfying diagnostic performance of 100% positive of detecting P. jirovecii from bronchoalveolar lavage (BAL) specimens in forty-six patients with non-HIV PCP, compared to only 15.2% for Gomori Methenamine silver (GMS) staining and 84.8% for Serum 1,3-beta-D-glucan (BDG). Among them, the mean age was 46.4-year-old (range 18–79-year-old) and mortality rate was 43.5%. The dominant underlying conditions were connective tissue diseases (34.8%), autoimmune kidney diseases (30.4%), followed by hematologic malignancies (10.9%), and solid organ transplantation (6.5%). A total of 38 cases (82.6%) received glucocorticoid and 19 cases (41.3%) used immunosuppressant within 3 months before diagnosed PCP. Multiple infections were very common, over two thirds' cases had mixed infections. Compared with survivors, non-survivors had a higher acute physiology and chronic health evaluation II (APACHE II) score (14.4 ± 4.8 vs. 10 ± 3.4), Procalcitonin (PCT) [ng/ml: 0.737 (0.122–1.6) vs. 0.23 (0.095–0.35)], lactic dehydrogenase (LDH) [U/L: 1372 (825.5–2150) vs. 739 (490.5–956)], and neutrophil-lymphocyte ratio (NLR) [21.6 (15.67–38.2) vs. 11.75 (5.1–15.52)], but had a lower PaO2/FiO2 ratio (mmHg:108.8 ± 42.4 vs. 150.5 ± 47.5), lymphocytes [×109/L: 0.33 (0.135–0.615) vs. 0.69 (0.325–1.07)] and CD4+ T cells [cell/μl: 112 (53.5–264) vs. 255 (145–303.5)], all P < 0.05. Furthermore, we found non-survivors' PaO2/FiO2 ratio of day 3 and day 7 had not improved when compared with that of day one, and platelet level and NLR became worse. Multivariate analysis showed that other pathogens' co-infection (OR = 9.011, 95% CI was 1.052–77.161, P = 0.045) and NLR (OR = 1.283, 95% CI was 1.046–1.547, P = 0.017) were the independent risk factors of poor prognosis. Conclusion mNGS is a very sensitive diagnostic tool for identifying P. jirovecii in patients who are non-HIV immunocompromised. PCP in patients who are non-HIV infected is associated with a high rate of multiple infections and severe condition. Mixed infection and elevation of NLR were the independent risk factors of poor prognosis.
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Ju CR, Lian QY, Guan WJ, Chen A, Zhang JH, Xu X, Chen RC, Li SY, He JX. Metagenomic Next-Generation Sequencing for Diagnosing Infections in Lung Transplant Recipients: A Retrospective Study. Transpl Int 2022; 35:10265. [PMID: 35221789 PMCID: PMC8866178 DOI: 10.3389/ti.2022.10265] [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: 11/25/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022]
Abstract
Background: Accurate identification of pathogens is essential for the diagnosis and control of infections. We aimed to compare the diagnostic performance of metagenomic next-generation sequencing (mNGS) and conventional detection methods (CDM) in lung transplant recipients (LTRs).Methods: We retrospectively analyzed 107 LTRs with suspected infection of pulmonary, blood, central nervous system or chest wall between March 2018 and November 2020. Bronchoalveolar lavage fluid and other body fluids were subject to pathogen detection by both mNGS and CDM.Results: Of the 163 specimens, 84 (51.5%) tested positive for both mNGS and culture, 19 (11.7%) of which were completely consistent, 44 (27.0%) were partially congruent, and 21 (12.9%) were discordant (kappa = .215; p = .001). Compared with CDM, mNGS detected a higher diversity of pathogens. Moreover, the turn-around time was significantly shorter for mNGS compared with culture (2.7 ± .4 vs. 5.5 ± 1.6 days, p < .001). As an auxiliary method, treatment strategies were adjusted according to mNGS findings in 31 cases (29.0%), including eight patients with non-infectious diseases, who were finally cured.Conclusion: mNGS can identify pathogens with a shorter turn-around time and therefore provide a more accurate and timely diagnostic information to ascertaining pulmonary infections. mNGS might have a role in differentiating infectious from non-infectious lung diseases in LTRs.
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Affiliation(s)
- Chun-Rong Ju
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiao-Yan Lian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Heng Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xin Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Thoracic Surgery, Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rong-Chang Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, China
| | - Shi-Yue Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Shi-Yue Li, ; Jian-Xing He,
| | - Jian-Xing He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Thoracic Surgery, Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Shi-Yue Li, ; Jian-Xing He,
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Liu L, Yuan M, Shi Y, Su X. Clinical Performance of BAL Metagenomic Next-Generation Sequence and Serum (1,3)-β-D-Glucan for Differential Diagnosis of Pneumocystis jirovecii Pneumonia and Pneumocystis jirovecii Colonisation. Front Cell Infect Microbiol 2022; 11:784236. [PMID: 35004353 PMCID: PMC8727434 DOI: 10.3389/fcimb.2021.784236] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022] Open
Abstract
Background Differentiating Pneumocystis jirovecii infection from colonisation is crucial for appropriate therapy administration. In this study, we evaluated the performance of bronchoalveolar lavage fluid (BAL) metagenomic next-generation sequencing (mNGS) and serum 1,3-β-D-glucan (BDG) tests in differentiating colonisation and infection with P. jirovecii. Methods From January 2018 to March 2021, 47 patients were enrolled in this study at the Hunan Provincial People’s Hospital. The final diagnosis was used as a reference, and cases were classified into the P. jirovecii pneumonia (PJP) group or the P. jirovecii colonisation (PJC) group. Clinical data were recorded. The performances of mNGS and BDG were compared. Result The fungal load significantly differed between patients with PJP and PJC, with median reads of 3,215.79 ± 1,797 vs. 5.61 ± 0.88 in the PJP and PJC groups, respectively (P < 0.0001). BDG also significantly differed between the two groups, with a median titre of 233.60 ± 39.65 pg/ml in the PJP group and 68.48 ± 19.21 pg/ml in the PJC group (P = 0.0006). The area under the curve was 0.973 (95%CI: 0.868–1.007) for mNGS of the BAL and 0.879 (95%CI: 0.769–0.989) for the serum BDG. The optimal threshold value for discriminating P. jirovecii infection from colonisation appeared to be 14 reads (sensitivity, 83.3%; specificity, 95.7%; positive likelihood ratio, 19.2) and BDG = 88.6 pg/ml (sensitivity, 79.2%; specificity, 92.9%; positive likelihood ratio, 18.2). No correlation between mNGS reads and the BDG titre was found in mNGS-positive patients (r2 = 0.0076, P = 0.583). The levels of lactate dehydrogenase and C-reactive protein were significantly higher in the PJP group than in the PJC group. Conclusion BAL mNGS and serum BDG are useful adjunct tests that can assist with differentiating between colonisation and infection of P. jirovecii.
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Affiliation(s)
- Li Liu
- Department of Infectious Disease, Hunan Provincial People's Hospital (The First Affiliated Hospital of Hunan Normal University), Changsha, China.,Department of Respiratory and Critical Care Medicine, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Mingjuan Yuan
- Department of Infectious Disease, The Central Hospital of Yueyang, Yueyang, China
| | - Yi Shi
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xin Su
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China.,Department of Respiratory and Critical Care Medicine, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
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Yu Q, Ding X, Wang W, Lou Y. Pneumocystis jiroveci pneumonia with cytomegalovirus infection diagnosed by metagenomic next-generation sequencing in a patient with nephrotic syndrome: A case report. Medicine (Baltimore) 2021; 100:e26842. [PMID: 34397856 PMCID: PMC8341323 DOI: 10.1097/md.0000000000026842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/19/2021] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Opportunistic infection with multiple pathogens currently has become less uncommon since the application of immunosuppressant or corticosteroid in non- Human immunodeficiency virus patients. However, the clinical diagnosis of the co-infection remains difficult since the uncertainty and deficiency of the microbiologic testing methods. PATIENT CONCERNS A 66-year-old male patient was admitted to our hospital with chest stuffiness, shortness of breath and elevated body temperature. DIAGNOSIS He was diagnosed with the co-infection of Pneumocystis jiroveci and cytomegalovirus by metagenomic next-generation sequencing of bronchoalveolar lavage fluid after bronchoscopy. INTERVENTIONS The patient was empirically treated with broad-spectrum antibiotics, trimethoprim/ sulfamethoxazole and ganciclovir in the beginning of the admission. OUTCOMES The condition of this patient was not improved even with the intervention at the early stage of the disease. His family requested discharge after 24 inpatient days. LESSONS This case highlights the application of metagenomic next-generation sequencing in the clinical diagnosis of pulmonary co-infection. Suitable prophylaxis, necessary clinical awareness and accurate diagnosis are indispensable for immunocompromised patients with pulmonary infection.
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Tsang CC, Teng JLL, Lau SKP, Woo PCY. Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing. J Fungi (Basel) 2021; 7:jof7080636. [PMID: 34436175 PMCID: PMC8398552 DOI: 10.3390/jof7080636] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have recently developed beyond the research realm and started to mature into clinical applications. Here, we review the current use of NGS for laboratory diagnosis of fungal infections. Since the first reported case in 2014, >300 cases of fungal infections diagnosed by NGS were described. Pneumocystis jirovecii is the predominant fungus reported, constituting ~25% of the fungi detected. In ~12.5% of the cases, more than one fungus was detected by NGS. For P. jirovecii infections diagnosed by NGS, all 91 patients suffered from pneumonia and only 1 was HIV-positive. This is very different from the general epidemiology of P. jirovecii infections, of which HIV infection is the most important risk factor. The epidemiology of Talaromyces marneffei infection diagnosed by NGS is also different from its general epidemiology, in that only 3/11 patients were HIV-positive. The major advantage of using NGS for laboratory diagnosis is that it can pick up all pathogens, particularly when initial microbiological investigations are unfruitful. When the cost of NGS is further reduced, expertise more widely available and other obstacles overcome, NGS would be a useful tool for laboratory diagnosis of fungal infections, particularly for difficult-to-grow fungi and cases with low fungal loads.
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Metagenomic Next-Generation Sequencing for the Diagnosis of Pneumocystis jirovecii Pneumonia in Non-HIV-Infected Patients: A Retrospective Study. Infect Dis Ther 2021; 10:1733-1745. [PMID: 34244957 PMCID: PMC8322252 DOI: 10.1007/s40121-021-00482-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/10/2021] [Indexed: 12/03/2022] Open
Abstract
Introduction This study aimed to evaluate the utility of metagenomic next-generation sequencing (mNGS) for the diagnosis of Pneumocystis jirovecii pneumonia (PJP) in non-human immunodeficiency virus-infected patients. Methods We conducted a retrospective study. A total of 60 non-human immunodeficiency virus-infected PJP patients and 134 patients diagnosed with non-PJP pneumonia were included. P. jirovecii and other co-pathogens identified by mNGS in bronchoalveolar lavage fluid and/or blood samples were analyzed. Using clinical composite diagnosis as the reference standard, we compared the diagnostic performance of mNGS in PJP with conventional methods, including Gomori methenamine silver staining and serum (1,3)-β-d-glucan. Modifications of antimicrobial treatment for PJP patients after the report of mNGS results were also reviewed. Results mNGS reached a sensitivity of 100% in diagnosing PJP, which was remarkably higher than Gomori methenamine silver staining (25.0%) and serum (1,3)-β-d-glucan (67.4%). The specificity of mNGS (96.3%) significantly surpassed serum (1,3)-β-d-glucan (81.4%). Simultaneous mNGS of bronchoalveolar lavage fluid and blood samples was performed in 21 out of 60 PJP patients, and it showed a concordance rate of 100% in detecting P. jirovecii. Besides, mNGS showed good performance in identifying co-pathogens of PJP patients, among which cytomegalovirus and Epstein-Barr virus were most commonly seen. Initial antimicrobial treatment was modified in 71.7% of PJP patients after the report of mNGS results. Conclusion mNGS is a useful diagnostic tool with good performance for the diagnosis of PJP and the detection of co-pathogens. mNGS of bronchoalveolar lavage fluid and/or blood samples is suggested in patients with presumptive diagnosis of PJP. Blood samples may be a good alternative to bronchoalveolar lavage fluid for mNGS when bronchoscopic examination is not feasible.
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Xu J, Yu Y, Lv J, Yang S, Wu J, Chen J, Peng W. Application of Metagenomic Next-Generation Sequencing to Diagnose Pneumocystis jirovecii Pneumonia in Kidney Transplantation Recipients. Ann Transplant 2021; 26:e931059. [PMID: 34099614 PMCID: PMC8196548 DOI: 10.12659/aot.931059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Pneumocystis jirovecii pneumonia (PJP) is one of the common opportunistic infections diagnosed in kidney transplantation recipients. It is difficult to identify early by use of classic tools such as Grocott-Gomori stains and polymerase chain reaction (PCR). Metagenomic next-generation sequencing (mNGS) is accurate, unbiased, and sensitive, and is promising in PJP diagnosis. Material/Methods Data on kidney transplantation patients diagnosed with PJP were retrospectively analyzed. The sensitivity and specificity of different tools such as mNGS, laboratory tests, and Grocott-Gomori stains for PJP diagnosis were compared. All recipients were treated with trimethoprim-sulfamethoxazole (TMP-SMX). Results There were a total of 12 kidney transplantation recipients diagnosed with PJP based on mNGS in our center from January 01, 2020 to October 27, 2020. Highly variable numbers of sequence reads for P. jiroveci (19 to 1041285) showed diagnostic significance. Bronchoalveolar lavage fluid (BALF) samples were tested by Grocott-Gomori staining, with only 6 of 11 (54.5%) positive. Other routine laboratory tests like routine blood tests, blood biochemistry, procalcitonin (PCT), immune function, (1,3)-β-d-glucan (BG), serum galactomannan (GM), and C-reactive protein (CRP) showed even lower efficacy. TMP-SMX appeared to be the ideal therapy for kidney transplantation recipients with PJP. Conclusions mNGS has utility in the diagnosis of PJP and mixed infections in kidney transplantation recipients, and TMP-SMX could be the ideal therapeutic drug for kidney transplantation recipients suffering from PJP.
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Affiliation(s)
- Jia Xu
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China (mainland).,National Key Clinical Department of Kidney Diseases, Hangzhou, Zhejiang, China (mainland).,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,The Third Grade Laboratory Under The National State, Administration of Traditional Chinese Medicine, Hangzhou, Zhejiang, China (mainland)
| | - Yedong Yu
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China (mainland).,National Key Clinical Department of Kidney Diseases, Hangzhou, Zhejiang, China (mainland).,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,The Third Grade Laboratory Under The National State, Administration of Traditional Chinese Medicine, Hangzhou, Zhejiang, China (mainland)
| | - Junhao Lv
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China (mainland).,National Key Clinical Department of Kidney Diseases, Hangzhou, Zhejiang, China (mainland).,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,The Third Grade Laboratory Under The National State, Administration of Traditional Chinese Medicine, Hangzhou, Zhejiang, China (mainland)
| | - Sisi Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China (mainland)
| | - Jianyong Wu
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China (mainland).,National Key Clinical Department of Kidney Diseases, Hangzhou, Zhejiang, China (mainland).,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,The Third Grade Laboratory Under The National State, Administration of Traditional Chinese Medicine, Hangzhou, Zhejiang, China (mainland)
| | - Jianghua Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China (mainland).,National Key Clinical Department of Kidney Diseases, Hangzhou, Zhejiang, China (mainland).,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,The Third Grade Laboratory Under The National State, Administration of Traditional Chinese Medicine, Hangzhou, Zhejiang, China (mainland)
| | - Wenhan Peng
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, Zhejiang, China (mainland).,National Key Clinical Department of Kidney Diseases, Hangzhou, Zhejiang, China (mainland).,Institute of Nephrology, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,The Third Grade Laboratory Under The National State, Administration of Traditional Chinese Medicine, Hangzhou, Zhejiang, China (mainland)
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Xie D, Xu W, You J, Yuan X, Li M, Bi X, Zhang K, Li H, Xian Y. Clinical descriptive analysis of severe Pneumocystis jirovecii pneumonia in renal transplantation recipients. Bioengineered 2021; 12:1264-1272. [PMID: 33896387 PMCID: PMC8806328 DOI: 10.1080/21655979.2021.1911203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pneumocystis jirovecii (P. jirovecii) pneumonia (PJP) is an opportunistic fungal infection after renal transplantation, which is always severe, difficult to diagnose, combined with multiple complications and have poor prognosis. We retrospectively analyzed clinical data, including risk factors, diagnosis, treatment and complications of seven clinical cases suffered with severe PJP after renal transplantation in our department in 2019. All the seven recipients were routinely prescribed with PJP prophylaxis after renal transplantation, and six of them suffered acute graft rejection before the infection. P. jirovecii sequence was identified in blood or broncho-alveolar lavage fluid (BALF) by the metagenomic next-generation sequencing (mNGS) in all patients. All the patients were improved with the therapy trimethoprim-sulfamethoxazole (TMP-SMX) combined with caspofungin for the PJP treatment, but suffered with complications including renal insufficiency, leukopenia, thrombocytopenia, gastrointestinal bleeding, mediastinalemphysema, pulmonary hemorrhage, and hemophagocytic syndrome and other severe infections. Taken together, mNGS is a powerful tool that could be used to diagnose PJP in renal transplantation recipients. And PJP prophylaxis should be prescribed during and after treatment for acute rejection. TMP-SMX is the first-line and effective drug for PJP treatment, but the complications are always life-threatening and lead to poor prognosis. We should pay attention to these life-threatening complications.
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Affiliation(s)
- Dan Xie
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Wen Xu
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jingya You
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiaofeng Yuan
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Mingliang Li
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiaogang Bi
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Kouxing Zhang
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Heng Li
- Department of Kidney Transplantation, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ying Xian
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
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22
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Application of metagenomic next-generation sequencing in the diagnosis and treatment guidance of Pneumocystis jirovecii pneumonia in renal transplant recipients. Eur J Clin Microbiol Infect Dis 2021; 40:1933-1942. [PMID: 33880744 PMCID: PMC8057919 DOI: 10.1007/s10096-021-04254-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/13/2021] [Indexed: 11/19/2022]
Abstract
Pneumocystis jirovecii pneumonia (PJP) is difficult to be diagnosed, so this study explored if PJP could be diagnosed by metagenomic next-generation sequencing (mNGS) and if mNGS could guide the therapy of PJP. mNGS was successfully diagnosed 13 out of 14 PJP recipients with 11 through peripheral blood samples, verified by PCR. Ten non-PJP recipients were enrolled as the control group. Blood tests revealed a high β-D-glucan (BDG) level in all recipients with PJP during the hospitalization. Four (28.6%) of 14 PJP patients were infected with cytomegalovirus simultaneously, while 8 (57.1%) suffered from a combined infection caused by Torque teno virus. Five (35.7%) of 14 cases died of PJP or the subsequent bacteremias/bacterial pneumonia with a longer interval between the onset and diagnosis of/the available therapy against PJP than survival cases. Univariate analysis of characteristics between PJP and non-PJP recipients revealed that BDG assays was higher at the admission in PJP group (P =0.011). This present study supports the value of mNGS detection of blood sample in diagnosing PJP, which could assist clinical decision for therapy against PJ and improve outcome of PJP. The study also highlights the sensitivity of BDG assays. Cytomegalovirus and Torque teno virus infections often occur at the same time of PJP, thus can be alerts of PJP.
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Xie D, Xian Y, You J, Xu W, Fan M, Bi X, Zhang K. Co-Infection Pneumonia with Mycobacterium abscessus and Pneumocystis jiroveci in a Patient without HIV Infection Diagnosed by Metagenomic Next-Generation Sequencing. Infect Drug Resist 2021; 14:879-888. [PMID: 33692629 PMCID: PMC7939513 DOI: 10.2147/idr.s292768] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/13/2021] [Indexed: 02/02/2023] Open
Abstract
Introduction Co-infection pneumonia with Mycobacterium abscessus (M. abscessus) and Pneumocystis jirovecii (P. jirovecii) is rarely reported in previously healthy patients without HIV infection. The diagnosis of pneumonia of M. abscessus and P. jirovecii remains challenging due to its nonspecific clinical presentation and the inadequate performance of conventional diagnostic methods. Case Report We report the case of a 44-year-old previously healthy male transferred to our hospital in February 2020 with a 4-month history of productive cough and one month of intermittent fever. At local hospital, the metagenomic next-generation sequencing(mNGS) detected P. jirovecii sequences in blood; with the antifungal therapy (Caspofungin, trimethoprim–sulfamethoxazole [TMP-SMX] and methylprednisolone [MP]), the patient still had hypoxemia, cough and fever. Then he was transferred to our hospital, the mNGS of bronchoalveolar lavage fluid (BALF) detected the sequences of M. abscessus and P. jirovecii. CD4+ T-lymphocytopenia in the peripheral blood cells was presented and HIV serology was negative. Caspofungin, TMP-SMX, clindamycin and MP were used to treat P. jirovecii pneumonia (PJP). Moxifloxacin, imipenem cilastatin and linezolid were used to treat M. abscessus infection. Clinical progress was satisfactory following antifungal combined with anti-M. abscessus therapy. Conclusion Co-infection pneumonia with M. abscessus and P. jirovecii as reported here is exceptionally rare. mNGS is a powerful tool for pathogen detection. M. abscessus infection could be a risk factor for P. jirovecii infection. This case report supports the value of mNGS in diagnosing of M. abscessus and P. jirovecii, and highlights the inadequacies of conventional diagnostic methods.
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Affiliation(s)
- Dan Xie
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Ying Xian
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Jingya You
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Wen Xu
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Min Fan
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Xiaogang Bi
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Kouxing Zhang
- Department of General Intensive Care Unit, Lingnan Hospital, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
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Yang P, Zhu X, Liang W, Cai R. The risk factor analysis and treatment experience in pneumocystis jirovecii pneumonia after kidney transplantation. Mycoses 2021; 64:495-502. [PMID: 33368732 DOI: 10.1111/myc.13235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 11/25/2020] [Accepted: 12/18/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Pneumocystis jirovecii pneumonia (PJP) is an opportunistic infection among solid organ transplantation. The occurrence of PJP is dangerous and fatal if there is no early identification and sufficient treatment. OBJECTIVE The aim of this study was to evaluate the risk factors and provide appropriate strategies of prophylaxis and treatment for PJP after kidney transplantation in our centre. PATIENTS/METHODS From January 2009 to December 2018, a total of 167 kidney transplantation recipients with pneumonia were enrolled, including 47 PJP patients as PJP group and 120 non-PJP patients as control group. The clinical characteristics of the two groups were analysed retrospectively. RESULTS Multivariate analysis showed that high total dosage of ATG [OR, 2.03; 95% CI, 1.12-3.68] and cytomegalovirus (CMV) infection were independent risk factors for PJP. Trimethoprim-sulfamethoxazole (TMP-SMX) (1.44 g q6h)-based treatment was used for 2 weeks, and its dosage and course were adjusted according to the therapeutic effect and side effects. Forty-five cases were recovered after 3 months of follow-up, and two patients died of respiratory failure. TMP-SMX (0.48 g/day) prophylaxis was used for 3-6 months and prolonged to 7-8 months after treatment for acute rejection, which reduced the incidence of PJP compared with those without prophylaxis. CONCLUSION Our study suggests that the high total dosage of ATG and CMV infection indicate the increased risk of PJP. The strategies of prophylaxis and treatment for PJP after kidney transplantation in our centre were effective.
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Affiliation(s)
- Pengfeng Yang
- Department of Ultrasound Medicine, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoqiu Zhu
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weixiang Liang
- Department of Ultrasound Medicine, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ruiming Cai
- Department of Renal Transplantation, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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