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Fu R, Xu J, Fan Z, Qu H, Jiang Y, Xiong W, Huang F, Xuan L, Xu N, Liu H, Wang Z, Sun J, Liu Q, Lin R. Metagenomic Next-generation Sequencing in the Diagnosis of Pulmonary Infections After Allogeneic Hematopoietic Stem Cell Transplantation. Transplant Cell Ther 2024:S2666-6367(24)00607-9. [PMID: 39197493 DOI: 10.1016/j.jtct.2024.08.014] [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: 05/25/2024] [Revised: 07/27/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024]
Abstract
BACKGROUND Early and accurate identification of pathogens is still challenging in pulmonary infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). The clinical usefulness of metagenomic next-generation sequencing (mNGS) remains under discussion in diagnosis of pulmonary infections after allo-HSCT. METHODS This multi-center retrospective study was conducted to compare mNGS and conventional microbiological tests (CMTs) in investigating the pathogens of pulmonary infections in allo-HSCT recipients. A hundred and forty allo-HSCT recipients with suspected pulmonary infections who underwent bronchoscopy were included. mNGS and CMTs were performed in BALF. RESULTS Among 140 allo-HSCT recipients with suspected pulmonary infections, the positive rate of mNGS was 71.4% whereas the positive rate of CMTs was 55.0%. mNGS identified 182 pathogens included bacteria (n = 88), fungi (n = 35) and viruses (n = 59) while 106 pathogens were detected by CMTs included bacteria (n = 31), fungi (n = 24) and viruses (n = 51). Ninety-eight patients were finally diagnosed as pulmonary infections, including 22 bacterial infections, 7 fungal,18 viral, 48 mixed infections, and 3 with unknown pathogen. Mixed infections were identified in 50.5% of the patients with pulmonary infection. The sensitivity of mNGS and CMTs for diagnosing pulmonary infections were 88.8% and 69.4%, respectively (P=0.001) while the specificity were 81.0% and 85.7%, respectively (P = 0.688). CONCLUSIONS mNGS might be a promising technology for diagnosis of pulmonary infections in the recipients of allo-HSCT.
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Affiliation(s)
- Rong Fu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Jun Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Zhiping Fan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Hong Qu
- Guangzhou Panyu Central Hospital, Infection Medicine Research Institute of Panyu District, Guangzhou, China
| | | | - Wenjie Xiong
- Foresea Life Insurance Guangzhou General Hospital, Guangzhou, China
| | - Fen Huang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Li Xuan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Na Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Hui Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Zhixiang Wang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Jing Sun
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China.
| | - Ren Lin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, 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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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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Liu Y, Li Z, Fu H, Ruan W, Wang H, Ding Y, Zhang M. The first case report: diagnosis and management of necrotizing fusobacterium lung abscess via BALF next-generation sequencing. BMC Infect Dis 2024; 24:218. [PMID: 38373919 PMCID: PMC10875748 DOI: 10.1186/s12879-024-09087-5] [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: 12/24/2023] [Accepted: 02/02/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Fusobacterium necrophorum (F. necrophorum)-induced necrotizing pneumonia is a rare but severe pulmonary infection. Insufficient microbiological detection methods can lead to diagnostic difficulties. METHODS We report a case of F. necrophorum lung abscess diagnosed by next-generation sequencing (NGS) of bronchoalveolar lavage fluid (BALF). RESULTS BALF-NGS detected F. necrophorum, guiding subsequent targeted antibiotic therapy. With active drainage and metronidazole treatment, the patient's condition was effectively treated. CONCLUSION BALF-NGS is a valuable tool for the rapid diagnosis of infections caused by difficult-to-culture bacteria. It played a decisive role in the early identification of F. necrophorum, enabling timely and targeted antibiotic intervention. Early diagnosis and appropriate treatment are crucial for the management of F. necrophorum pneumonia.
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Affiliation(s)
- Yang Liu
- Respiratory Department, Shaoxing City Keqiao District Hospital of Traditional Chinese Medicine, 312030, Shaoxing, China.
| | - Ziye Li
- Respiratory Department, Shaoxing City Keqiao District Hospital of Traditional Chinese Medicine, 312030, Shaoxing, China
| | - Handan Fu
- Respiratory Department, Shaoxing City Keqiao District Hospital of Traditional Chinese Medicine, 312030, Shaoxing, China
| | - Weiliang Ruan
- Respiratory Department, Shaoxing City Keqiao District Hospital of Traditional Chinese Medicine, 312030, Shaoxing, China
| | - Hua Wang
- Special Inspection Department, Shaoxing City Keqiao District Hospital of Traditional Chinese Medicine, 312030, Shaoxing, China
| | - Yuhong Ding
- Respiratory Department, Shaoxing City Keqiao District Hospital of Traditional Chinese Medicine, 312030, Shaoxing, China
| | - Miao Zhang
- Radiology Department, Shaoxing City Keqiao District Hospital of Traditional Chinese Medicine, 312030, Shaoxing, 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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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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Zhang K, Bai YZ, Liu C, Liu SS, Lu XX, Yang RG. Composition of pathogenic microorganism in chronic osteomyelitis based on metagenomic sequencing and its application value in etiological diagnosis. BMC Microbiol 2023; 23:313. [PMID: 37891467 PMCID: PMC10612345 DOI: 10.1186/s12866-023-03046-x] [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: 08/06/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Traditionally, conventional microbiological culture methods have been used to detect pathogenic microorganisms in chronic osteomyelitis. However, these methods have been found to have a low detection rate, complicating the precise guidance of infection treatment. This study employed metagenomic next-generation sequencing (mNGS) to detect these microorganisms in chronic osteomyelitis with three main objectives: 1). Gain a deeper understanding of the composition of pathogenic microorganisms in chronic osteomyelitis. 2). Compare the microbial detection rates between mNGS and the standard culture methods used in laboratories to enhance the effectiveness of the traditional culture methods. 3). Explore the potential of mNGS in etiological diagnosis. METHODS Fifty clinically confirmed intraoperative bone tissue samples of chronic osteomyelitis from January 2021 to December 2021 were collected and subjected to mNGS and microbiological testing, respectively. The orthopaedic surgeon combined clinical manifestations and related examinations to determine the causative pathogens. RESULTS The culture method obtained 29 aerobic and parthenogenic anaerobic bacteria, 3 specific anaerobic bacteria, and 1 yeast-like fungus. Thirty-six aerobic and parthenogenic anaerobic bacteria, 11 specific anaerobic bacteria, and 1 yeast-like fungus were obtained by mNGS, and 2 Mycobacterium tuberculosis(MTB) strains were detected. However, there was no significant difference in the overall positive detection rate between mNGS and the culture method (P = 0.07), and the two were not statistically significant in detecting aerobic and partly anaerobic bacteria (P = 0.625). But, mNGS was significantly superior to culture in detecting anaerobic bacteria and Mycobacterium tuberculosis (P<0.05). CONCLUSIONS The mNGS method has enhanced our understanding of the distribution of pathogenic microorganisms in chronic osteomyelitis. Traditional culture methods help isolate and cultivate aerobic and facultative anaerobic bacteria, and fungi, and are also utilized for antibacterial drug sensitivity tests. However, mNGS has shown superior capabilities in detecting anaerobic bacteria, MTB, and mixed infection bacteria. This finding offers invaluable guidance for improving laboratory microbial culture and detection conditions. Hence, mNGS should be judiciously used for chronic osteomyelitis, and PCR can be implemented for certain difficult-to-culture microorganisms, such as MTB.
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Affiliation(s)
- Kang Zhang
- Laboratory Medicine of Beijing Tongren Hospital affiliated to Capital Medical University, Beijing, China
| | - Yu-Zhe Bai
- Department of Tissue Repair and Regeneration, The First Medical Center of PLA General Hospital, Beijing, China
| | - Chang Liu
- Clinical Laboratory of Tsinghua University Hospital, Beijing, China
| | - Shan-Shan Liu
- Laboratory Medicine of Beijing Tongren Hospital affiliated to Capital Medical University, Beijing, China
| | - Xin-Xin Lu
- Laboratory Medicine of Beijing Tongren Hospital affiliated to Capital Medical University, Beijing, China.
| | - Run-Gong Yang
- Department of Tissue Repair and Regeneration, The First Medical Center of PLA General Hospital, Beijing, 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: 3] [Impact Index Per Article: 3.0] [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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9
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Shen H, Liu T, Shen M, Zhang Y, Chen W, Chen H, Wang Y, Liu J, Tao J, He L, Lu G, Yan G. Utilizing metagenomic next-generation sequencing for diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid in pediatric intensive care unit: results from a large real-world cohort. Front Cell Infect Microbiol 2023; 13:1200806. [PMID: 37655299 PMCID: PMC10466250 DOI: 10.3389/fcimb.2023.1200806] [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: 04/05/2023] [Accepted: 07/27/2023] [Indexed: 09/02/2023] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection in various infections. In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of pneumonia in pediatric intensive care units (PICU) using bronchoalveolar lavage fluid (BALF) samples. Methods A total of 104 pediatric patients with pneumonia who were admitted into PICU between June 2018 and February 2020 were retrospectively enrolled. Among them, 101 subjects who had intact clinical information were subject to parallel comparison of mNGS and conventional microbiological tests (CMTs) for pathogen detection. The performance was also evaluated and compared between BALF-mNGS and BALF-culture methods. Moreover, the diversity and structure of all 104 patients' lung BALF microbiomes were explored using the mNGS data. Results Combining the findings of mNGS and CMTs, 94.06% (95/101) pneumonia cases showed evidence of causative pathogenic infections, including 79.21% (80/101) mixed and 14.85% (15/101) single infections. Regarding the pathogenesis of pneumonia in the PICU, the fungal detection rates were significantly higher in patients with immunodeficiency (55.56% vs. 25.30%, P =0.025) and comorbidities (40.30% vs. 11.76%, P=0.007). There were no significant differences in the α-diversity either between patients with CAP and HAP or between patients with and without immunodeficiency. Regarding the diagnostic performance, the detection rate of DNA-based BALF-mNGS was slightly higher than that of the BALF-culture although statistically insignificant (81.82% vs.77.92%, P=0.677) and was comparable to CMTs (81.82% vs. 89.61%, P=0.211). The overall sensitivity of DNA-based mNGS was 85.14% (95% confidence interval [CI]: 74.96%-92.34%). The detection rate of RNA-based BALF-mNGS was the same with CMTs (80.00% vs 80.00%, P>0.999) and higher than BALF-culture (80.00% vs 52.00%, P=0.045), with a sensitivity of 90.91% (95%CI: 70.84%-98.88%). Conclusions mNGS is valuable in the etiological diagnosis of pneumonia, especially in fungal infections, and can reveal pulmonary microecological characteristics. For pneumonia patients in PICU, the mNGS should be implemented early and complementary to CMTs.
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Affiliation(s)
- Huili Shen
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Tingyan Liu
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Meili Shen
- Medical Department, Nanjing Dinfectome Technology Inc., Nanjing, Jiangsu, China
| | - Yi Zhang
- Department of Clinical Epidemiology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Weiming Chen
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Hanlin Chen
- Medical Department, Nanjing Dinfectome Technology Inc., Nanjing, Jiangsu, China
| | - Yixue Wang
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Jing Liu
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Jinhao Tao
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Liming He
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Guoping Lu
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Gangfeng Yan
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
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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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Liao H, Zhu M, Cheng Z. Epstein-Barr virus (EBV) induced pneumonitis in a patient with breast cancer receiving neoadjuvant chemotherapy: A case report. Respir Med Case Rep 2023; 45:101849. [PMID: 37448884 PMCID: PMC10336251 DOI: 10.1016/j.rmcr.2023.101849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/28/2023] [Accepted: 04/09/2023] [Indexed: 07/15/2023] Open
Abstract
Background Epstein-Barr virus (EBV) usually leads to latent infection and is reported mostly in infectious mononucleosis, lymphoma, and cancer in adolescents and adults, but pneumonitis due to EBV infection in adults is rare. Case presentation We hereby reported a case of a 52-year-old woman with breast cancer who developed acute pneumonia during neoadjuvant chemotherapy. Her serologic workup revealed a low CD4+ count and positive anti-EBV antibodies. Chest computed tomography (CT) shows multiple patchy ground-glass shadows in the bilateral lung. Microscopic examination of stained sputum and bronchoalveolar lavage fluid (BALF) smear specimens did not find any pathogens. Metagenomic next-generation sequencing (mNGS) of BALF indicated a large number of EBV reads, allowing to confirm the diagnosis of EBV induced pneumonitis. The patient was then treated with ganciclovir with subsequent dramatic clinical and radiological improvement. Conclusions This case highlights the combined application of mNGS and traditional tests in the clinical diagnosis of invasive pulmonary infection. In the meanwhile, clinicians should be aware neoadjuvant chemotherapy for breast cancer carries a risk of EBV induced pneumonitis, so that EBV induced pneumonitis could be considered in differential diagnosis while similar patients present, to orchestrate improvements in diagnosis, treatment, and prognosis.
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Weise DO, Kruk ME, Higgins L, Markowski TW, Jagtap PD, Mehta S, Mickelson A, Parker LL, Wendt CH, Griffin TJ. An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples. Clin Proteomics 2023; 20:14. [PMID: 37005570 PMCID: PMC10068177 DOI: 10.1186/s12014-023-09404-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/13/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUND Clinical bronchoalveolar lavage fluid (BALF) samples are rich in biomolecules, including proteins, and useful for molecular studies of lung health and disease. However, mass spectrometry (MS)-based proteomic analysis of BALF is challenged by the dynamic range of protein abundance, and potential for interfering contaminants. A robust, MS-based proteomics compatible sample preparation workflow for BALF samples, including those of small and large volume, would be useful for many researchers. RESULTS We have developed a workflow that combines high abundance protein depletion, protein trapping, clean-up, and in-situ tryptic digestion, that is compatible with either qualitative or quantitative MS-based proteomic analysis. The workflow includes a value-added collection of endogenous peptides for peptidomic analysis of BALF samples, if desired, as well as amenability to offline semi-preparative or microscale fractionation of complex peptide mixtures prior to LC-MS/MS analysis, for increased depth of analysis. We demonstrate the effectiveness of this workflow on BALF samples collected from COPD patients, including for smaller sample volumes of 1-5 mL that are commonly available from the clinic. We also demonstrate the repeatability of the workflow as an indicator of its utility for quantitative proteomic studies. CONCLUSIONS Overall, our described workflow consistently provided high quality proteins and tryptic peptides for MS analysis. It should enable researchers to apply MS-based proteomics to a wide-variety of studies focused on BALF clinical specimens.
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Affiliation(s)
- Danielle O Weise
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Medical School, University of Minnesota, Minneapolis, MN, USA
| | - Monica E Kruk
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Medical School, University of Minnesota, Minneapolis, MN, USA
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Todd W Markowski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Alan Mickelson
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Medical School, University of Minnesota, Minneapolis, MN, USA
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Christine H Wendt
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Medical School, University of Minnesota, Minneapolis, MN, USA
- Minneapolis VA Health Care System, Minneapolis, MN, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
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Xiao YH, Liu MF, Wu H, Xu DR, Zhao R. Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing for Pathogen Detection in Patients with Suspected Infectious Diseases: A Retrospective Study from a Large Tertiary Hospital. Infect Drug Resist 2023; 16:1815-1828. [PMID: 37016633 PMCID: PMC10066896 DOI: 10.2147/idr.s401707] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Purpose Metagenomic next-generation sequencing (mNGS) is a powerful yet unbiased method to identify pathogens in suspected infections. However, little is known about its clinical effectiveness. The present study aimed to assess the efficacy of mNGS in routine clinical practice. Patients and Methods In this single-center retrospective cohort study, 518 patients with suspected infectious diseases were assessed for inclusion. Among them, each patient had undergone mNGS testing; 407 patients had undergone both microbial culture and mNGS testing. The result of mNGS testing was compared to microbial culture performed concurrently. The diagnostic performance of mNGS was evaluated using the comprehensive clinical diagnosis as the reference standard. Results There was a significant difference in the positive detection rates of pathogens between mNGS and culture (331/407, 81.3% vs 79/407, 19.4%, P < 0.001). The sensitivity of mNGS was much higher than the culture method (79.5% vs 21.3%, P < 0.001), especially in sample types of sputum and bronchoalveolar lavage fluid (BALF). Notably, the sensitivity of blood mNGS was relatively lower than other sample types (67.4% vs 88.9-93.8%). Pathogen cfDNA load based on standardized stringently mapped read number at the species level of microorganisms (SDSMRN) was significantly lower in blood than in other sample types from the same patient (P = 0.0003). Importantly, mNGS directly led to a change of treatment regimen in 142 (27.4%) cases, including antibiotic escalation (15.3%), antibiotic de-escalation (9.1%), and early definitive diagnosis to initiate appropriate treatment (3.1%). Conclusion Our in-house mNGS platform significantly improved the sensitivity for the diagnosis of infectious diseases. mNGS has the potential to improve clinical outcomes by optimizing antimicrobial therapy.
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Affiliation(s)
- Yang-Hua Xiao
- Department of Clinical Laboratory, Medical Center for Burn and Plastic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
- School of Public Health, Nanchang University, Nanchang, People’s Republic of China
| | - Mei-Fang Liu
- Department of Clinical Laboratory, Medical Center for Burn and Plastic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Hongwen Wu
- Department of Clinical Laboratory, Medical Center for Burn and Plastic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
- Department of Medical Instruments, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - De-Rong Xu
- Department of Clinical Laboratory, Medical Center for Burn and Plastic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
- Correspondence: De-Rong Xu; Rui Zhao, Email ;
| | - Rui Zhao
- Department of Clinical Laboratory, Medical Center for Burn and Plastic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
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Xie Y, Dai B, Zhou X, Liu H, Wu W, Yu F, Zhu B. Diagnostic Value of Metagenomic Next-Generation Sequencing for Multi-Pathogenic Pneumonia in HIV-Infected Patients. Infect Drug Resist 2023; 16:607-618. [PMID: 36733920 PMCID: PMC9888013 DOI: 10.2147/idr.s394265] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/05/2023] [Indexed: 01/28/2023] Open
Abstract
Background To evaluate the value and challenges of real-world clinical application of metagenomic next-generation sequencing (mNGS) for bronchoalveolar lavage fluid (BALF) in HIV-infected patients with suspected multi-pathogenic pneumonia. Methods Fifty-seven HIV-infected patients with suspected mixed pneumonia who were agreed to undergo the bronchoscopy were recruited and retrospectively reviewed the results of mNGS and conventional microbiological tests (CMTs) of BALF from July 2020 to June 2022. Results 54 patients were diagnosed with pneumonia including 49 patients with definite pathogens and five patients with probable pathogens. mNGS exhibited a higher diagnostic accuracy for fungal detection than CMTs in HIV-infected patients with suspected pulmonary infection. The sensitivity of mNGS in diagnosis of pneumonia in HIV-infected patients was much higher than that of CMTs (79.6% vs 61.1%; P < 0.05). Patients with mixed infection had lower CD4 T-cell count and higher symptom duration before admitting to the hospital than those with single infection. The detection rate of mNGS for mixed infection was significantly higher than that of CMTs and more co-pathogens could be identified by mNGS. The most common pattern of mixed infection observed was fungi-virus (11/29, 37.9%), followed by fungi-virus-bacteria (6/29, 20.7%) coinfection in HIV-infected patients with multi-pathogenic pneumonia. Conclusion mNGS improved the pathogens detection rate and exhibited advantages in identifying multi-pathogenic pneumonia in HIV-infected patients. Early performance of bronchoscopy and mNGS are recommended in HIV-infected patients with low CD4 T cell counts and long duration of symptoms. The most common pattern of mixed infection observed was fungi-virus, followed by fungi-virus-bacteria coinfection in HIV infected patients with multi-pathogenic pneumonia.
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Affiliation(s)
- Yirui Xie
- 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 Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of China,Correspondence: Yirui Xie; Biao Zhu, 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 Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79, QingChun Road, Hangzhou, 310003, People’s Republic of China, Tel/Fax +86-571-87236416, Email ;
| | - Bohao Dai
- 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 Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of China
| | - Xiaotang Zhou
- 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 Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of China
| | - Huiting Liu
- 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 Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of China
| | - Wei Wu
- 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, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of China
| | - Fei Yu
- Key Laboratory of Clinical in vitro Diagnostic Techniques of Zhejiang Province, Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, People’s Republic of China
| | - Biao Zhu
- 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 Department of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, People’s Republic of 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: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
OBJECTIVE The aim of this study was to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) for the diagnosis of Pneumocystis jirovecii Pneumonia (PCP) in critically pediatric patients. METHODS Seventeen critically pediatric patients with PCP and sixty patients diagnosed with non-PCP pneumonia who were admitted in pediatric intensive care unit between June 2018 and July 2021 were enrolled. Conventional methods and mNGS for detecting Pneumocystis jirovecii (P. jirovecii) were compared. The patients' demographics, comorbidities, laboratory test results, antibiotic treatment response and 30 day mortality were analyzed. RESULT The mNGS showed a satisfying diagnostic performance with a sensitivity of 100% in detecting P. jirovecii compared with Gomori methenamine silver staining (5.9%), serum (1,3)-β-D-glucan (86.7%) and and LDH (55.6%). The diagnostic specificity of mNGS for PCP was higher than that of serum BDG (56.7%) and LDH (71.4%). In PCP group, over one thirds' cases had mixed infections. Compared with survivors, non-survivors had higher stringently mapped read numbers (SMRNs) in bronchoalveolar lavage fluid (BALF) sample (P < 0.05), suggesting SMRNs were closely associated with the severity of response. The detection for P. jirovecii by mNGS both in BALF and blood samples reached a concordance rate of 100%, and the SMRNs in the BALF were remarkably higher than that in blood samples. Initial antimicrobial treatment was modified in 88.2% of PCP patients based on the mNGS results. CONCLUSION The mNGS is a potential and efficient technology in diagnosing PCP and shows a satisfying performance in the detection of co-pathogens. Both blood and BALF samples for mNGS are suggested for the presumptive diagnosis of PCP.
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Affiliation(s)
- Hengxin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Yujian Liang
- Department of Pediatric Intensive Care Unit, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Ruizhi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Yijie Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China
| | - Xiaoyun Zhang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China
| | - Hao Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Xuegao Yu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Mengzhi Hong
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Juhua Yang
- Vision Medicals Co., Ltd, Guangzhou, China
| | - Kang Liao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Hongxu Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Min Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
| | - Yili Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
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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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Deng W, Xu H, Wu Y, Li J. Diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in pediatric pneumonia. Front Cell Infect Microbiol 2022; 12:950531. [PMID: 36389175 PMCID: PMC9648200 DOI: 10.3389/fcimb.2022.950531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/26/2022] [Indexed: 07/25/2023] Open
Abstract
OBJECTIVES The aim of this study was to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) versus conventional microbiological tests (CMTs) for pediatric pneumonia. METHODS This retrospective observational study enrolled 103 children who were diagnosed with pneumonia and hospitalized at Hubei Maternity and Child Health Care Hospital between 15 October 2020 and 15 February 2022. The pneumonia diagnosis was based on clinical manifestations, lung imaging, and microbiological tests. Pathogens in the lower respiratory tract were detected using CMTs and BALF mNGS (of DNA and RNA). The diagnostic performance of BALF mNGS was compared with that of CMTs. RESULTS In 96 patients, pathogens were identified by microbiological tests. The overall pathogen detection rate of mNGS was significantly higher than that of CMTs (91.3% vs. 59.2%, p = 0.000). The diagnostic performance of mNGS varied for different pathogens; however, its sensitivity and accuracy for diagnosing bacterial and viral infections were both higher than those of CMTs (p = 0.000). For the diagnosis of fungi, the sensitivity of mNGS (87.5%) was higher than that of CMTs (25%); however, its specificity and accuracy were lower than those of CMTs (p < 0.01). For the diagnosis of Mycoplasma pneumoniae, the specificity (98.8%) and accuracy (88.3%) of mNGS were high; however, its sensitivity (42.1%) was significantly lower than that of CMTs (100%) (p = 0.001). In 96 patients with definite pathogens, 52 cases (50.5%) were infected with a single pathogen, while 44 cases (42.7%) had polymicrobial infections. Virus-bacteria and virus-virus co-infections were the most common. Staphylococcus aureus, Haemophilus influenzae, rhinovirus, cytomegalovirus, parainfluenza virus, and fungi were more likely to be associated with polymicrobial infections. CONCLUSIONS BALF mNGS improved the detection rate of pediatric pneumonia, especially in mixed infections. The diagnostic performance of BALF mNGS varies according to pathogen type. mNGS can be used to supplement CMTs. A combination of mNGS and CMTs may be the best diagnostic strategy.
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Affiliation(s)
- Wenhua Deng
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Huan Xu
- Department of Scientific Affairs, Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Yabin Wu
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Jie Li
- Pediatric Respiratory Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
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Wang C, You Z, Fu J, Chen S, Bai D, Zhao H, Song P, Jia X, Yuan X, Xu W, Zhao Q, Pang F. Application of metagenomic next-generation sequencing in the diagnosis of pulmonary invasive fungal disease. Front Cell Infect Microbiol 2022; 12:949505. [PMID: 36237437 PMCID: PMC9551268 DOI: 10.3389/fcimb.2022.949505] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/05/2022] [Indexed: 12/16/2022] Open
Abstract
BackgroundMetagenomic next-generation sequencing (mNGS) is increasingly being used to detect pathogens directly from clinical specimens. However, the optimal application of mNGS and subsequent result interpretation can be challenging. In addition, studies reporting the use of mNGS for the diagnosis of invasive fungal infections (IFIs) are rare.ObjectiveWe critically evaluated the performance of mNGS in the diagnosis of pulmonary IFIs, by conducting a multicenter retrospective analysis. The methodological strengths of mNGS were recognized, and diagnostic cutoffs were determined.MethodsA total of 310 patients with suspected pulmonary IFIs were included in this study. Conventional microbiological tests (CMTs) and mNGS were performed in parallel on the same set of samples. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the logarithm of reads per kilobase per million mapped reads [lg(RPKM)], and read counts were used to predict true-positive pathogens.ResultThe majority of the selected patients (86.5%) were immunocompromised. Twenty species of fungi were detected by mNGS, which was more than was achieved with standard culture methods. Peripheral blood lymphocyte and monocyte counts, as well as serum albumin levels, were significantly negatively correlated with fungal infection. In contrast, C-reactive protein and procalcitonin levels showed a significant positive correlation with fungal infection. ROC curves showed that mNGS [and especially lg(RPKM)] was superior to CMTs in its diagnostic performance. The area under the ROC curve value obtained for lg(RPKM) in the bronchoalveolar lavage fluid of patients with suspected pulmonary IFIs, used to predict true-positive pathogens, was 0.967, and the cutoff value calculated from the Youden index was −5.44.ConclusionsIn this study, we have evaluated the performance of mNGS-specific indicators that can identify pathogens in patients with IFIs more accurately and rapidly than CMTs, which will have important clinical implications.
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Affiliation(s)
- Chengtan Wang
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Zhiqing You
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Juanjuan Fu
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Shuai Chen
- Department of Clinical Laboratory, Liaocheng Third People’s Hospital, Liaocheng, China
- Department of Virology, School of Public Health, Shandong University, Jinan, China
| | - Di Bai
- Department of Clinical Laboratory, Liaocheng Third People’s Hospital, Liaocheng, China
| | - Hui Zhao
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Pingping Song
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Xiuqin Jia
- The Key Laboratory of Molecular Pharmacology, Liaocheng People’s Hospital, Liaocheng, China
| | - Xiaoju Yuan
- Department of Gastroenterology, Liaocheng People’s Hospital, Liaocheng, China
| | - Wenbin Xu
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
| | - Qigang Zhao
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
- *Correspondence: Feng Pang, ; Qigang Zhao,
| | - Feng Pang
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, China
- *Correspondence: Feng Pang, ; Qigang Zhao,
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