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Zou S, Chen Z, Tan Y, Tan M, Guo W, Wu S, Liu J, Song S, Peng Y, Wang M, Liang K. Microbiomes detected by cerebrospinal fluid metagenomic next-generation sequencing among patients with and without HIV with suspected central nervous system infection. HIV Med 2024; 25:794-804. [PMID: 38515324 DOI: 10.1111/hiv.13634] [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: 12/17/2023] [Accepted: 03/02/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Opportunistic infections in the central nervous system (CNS) can be a serious threat to people living with HIV. Early aetiological diagnosis and targeted treatment are crucial but difficult. Metagenomic next-generation sequencing (mNGS) has significant advantages over traditional detection methods. However, differences in the cerebrospinal fluid (CSF) microbiome profiles of patients living with and without HIV with suspected CNS infections using mNGS and conventional testing methods have not yet been adequately evaluated. METHODS We conducted a retrospective cohort study in the first hospital of Changsha between January 2019 and June 2022 to investigate the microbiomes detected using mNGS of the CSF of patients living with and without HIV with suspected CNS infections. The pathogens causing CNS infections were concurrently identified using both mNGS and traditional detection methods. The spectrum of pathogens identified was compared between the two groups. RESULTS Overall, 173 patients (140 with and 33 without HIV) with suspected CNS infection were enrolled in our study. In total, 106 (75.7%) patients with and 16 (48.5%) patients without HIV tested positive with mNGS (p = 0.002). Among the enrolled patients, 71 (50.7%) with HIV and five (15.2%) without HIV tested positive for two or more pathogens (p < 0.001). Patients with HIV had significantly higher proportions of fungus (20.7% vs. 3.0%, p = 0.016) and DNA virus (59.3% vs. 21.2%, p < 0.001) than those without HIV. Epstein-Barr virus (33.6%) was the most commonly identified potential pathogen in the CSF of patients living with HIV using mNGS, followed by cytomegalovirus (20.7%) and torque teno virus (13.8%). The top three causative pathogens identified in patients without HIV were Streptococcus (18.2%), Epstein-Barr virus (12.1%), and Mycobacterium tuberculosis (9.1%). In total, 113 patients living with HIV were diagnosed as having CNS infections. The rate of pathogen detection in people living with HIV with a CNS infection was significantly higher with mNGS than with conventional methods (93.8% vs. 15.0%, p < 0.001). CONCLUSION CSF microbiome profiles differ between patients living with and without HIV with suspected CNS infection. mNGS is a powerful tool for the diagnosis of CNS infection among people living with HIV, especially in those with mixed infections.
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Affiliation(s)
- Shi Zou
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhong Chen
- The Institute of HIV/AIDS, The First Hospital of Changsha, Changsha, China
| | - Yuting Tan
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Miao Tan
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wei Guo
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Pathology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Songjie Wu
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Department of Nosocomial Infection Management, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jie Liu
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Shihui Song
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongquan Peng
- Graduate Collaborative Training Base of the First Hospital of Changsha, Hengyang Medical School, Uni-versity of South China, Hengyang, China
| | - Min Wang
- The Institute of HIV/AIDS, The First Hospital of Changsha, Changsha, China
| | - Ke Liang
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Department of Nosocomial Infection Management, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan, China
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Yao A, Wang J, Xu Q, Shah BK, Sun K, Hu F, Wang C, Xie S. Higher diagnostic value of metagenomic next-generation sequencing in acute infection than chronic infection: a multicenter retrospective study. Front Microbiol 2024; 15:1295184. [PMID: 38351916 PMCID: PMC10864100 DOI: 10.3389/fmicb.2024.1295184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
Background The aim of this study is to compare the diagnostic value of metagenomic next-generation sequencing (mNGS) vs. conventional culture methods (CM) in chronic infection and acute infection. Methods We retrospectively analyzed the bronchoalveolar lavage fluid (BALF) of 88 patients with acute infection and 105 patients with chronic infection admitted to three hospitals from 2017 to 2022. Results The results showed that the sensitivity and specificity of mNGS were higher than those of CM. The number of patients who changed the antibiotic treatment in the mNGS positive group was larger than that of patients in the mNGS negative group in both the acute infection group (60.5 vs. 28.0%, P = 0.0022) and chronic infection group (46.2 vs. 22.6%, P = 0.01112). High levels of temperature (OR: 2.02, 95% CI: 1.18-3.70, P: 0.015), C-reactive protein (CRP) (OR: 15, 95% CI: 2.74-280.69, P: 0.011), neutrophil count (OR: 3.09, 95% CI: 1.19-8.43, P: 0.023), and low levels of lymphocyte count (OR: 3.43, 95% CI:1.26-10.21, P: 0.020) may lead to positive mNGS results in the acute infection group while no significant factor was identified to predict positive results in the chronic infection group. Conclusion mNGS could provide useful guidance on antibiotic strategies in infectious diseases and may be more valuable for the diagnosis and treatment of acute infection vs. chronic infection.
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Affiliation(s)
- Anjie Yao
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiale Wang
- School of Medicine, Tongji University, Shanghai, China
| | - Qintao Xu
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
- College of Medicine, Jinggangshan University, Ji'an, China
| | | | - Kai Sun
- Department of Respiratory Medicine, ChongMing Branch of Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feng Hu
- Department of Respiratory and Critical Care Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changhui Wang
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shuanshuan Xie
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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Liu L, Fan H, Li L, Fan Y. Acarbose reduces Pseudomonas aeruginosa respiratory tract infection in type 2 diabetic mice. Respir Res 2023; 24:312. [PMID: 38098038 PMCID: PMC10722695 DOI: 10.1186/s12931-023-02619-8] [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: 09/10/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is widely prevalent worldwide, and respiratory tract infections (RTIs) have become the primary cause of death for T2DM patients who develop concurrent infections. Among these, Pseudomonas aeruginosa infection has been found to exhibit a high mortality rate and poor prognosis and is frequently observed in bacterial infections that are concurrent with COVID-19. Studies have suggested that acarbose can be used to treat T2DM and reduce inflammation. Our objective was to explore the effect of acarbose on P. aeruginosa RTI in T2DM individuals and elucidate its underlying mechanism. METHODS High-fat diet (HFD) induction and P. aeruginosa inhalation were used to establish a RTI model in T2DM mice. The effect and mechanism of acarbose administered by gavage on P. aeruginosa RTI were investigated in T2DM and nondiabetic mice using survival curves, pathological examination, and transcriptomics. RESULTS We found that P. aeruginosa RTI was more severe in T2DM mice than in nondiabetic individuals, which could be attributed to the activation of the NF-κB and TREM-1 signaling pathways. When acarbose alleviated P. aeruginosa RTI in T2DM mice, both HIF-1α and NF-κB signaling pathways were inhibited. Furthermore, inhibition of the calcium ion signaling pathway and NF-κB signaling pathway contributed to the attenuation of P. aeruginosa RTI by acarbose in nondiabetic mice. CONCLUSIONS This study confirmed the attenuating effect of acarbose on P. aeruginosa RTIs in T2DM and nondiabetic mice and investigated its mechanism, providing novel support for its clinical application in related diseases.
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Affiliation(s)
- Lin Liu
- Department of Otolaryngology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, People's Republic of China
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Haiyang Fan
- Department of Otolaryngology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, People's Republic of China
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liang Li
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, People's Republic of China.
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Yunping Fan
- Department of Otolaryngology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, People's Republic of China.
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Huang F, Wang H, Qiao R, Peng Q, Zhao C, Miao L. Diagnostic accuracy and microbial profiles of tuberculous pleurisy: a comparative study of metagenomic next generation sequencing and GeneXpert Mycobacterium tuberculosis. Front Cell Infect Microbiol 2023; 13:1243441. [PMID: 38089819 PMCID: PMC10711093 DOI: 10.3389/fcimb.2023.1243441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction There is a clinical challenge in diagnosing tuberculous pleurisy accurately and promptly, highlighting the urgent need for a rapid and sensitive diagnostic method. This study aimed to evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) and GeneXpert Mycobacterium tuberculosis (MTB) for identifying tuberculous pleurisy and analyzing the microbial profiles of both tuberculous and non-tuberculous pleural effusions. Methods The study enrolled 31 patients with suspected tuberculous pleurisy, of which 15 were confirmed to have tuberculous pleurisy and subsequently allocated to the tuberculous pleurisy group (TP group), while the remaining 16 individuals were assigned to the non-tuberculous pleurisy group (NTP group). mNGS and GeneXpert MTB were performed on pleural effusion samples, and the diagnostic accuracy of both tests was compared. We employed established formulas to compute crucial indicators, including sensitivity, specificity, missed diagnosis rate, misdiagnosed rate, positive predictive value (PPV), and negative predictive value (NPV). Results The results showed that both tests had high specificity (100%) and positive predictive value (100%) for detecting tuberculous pleurisy, along with comparable sensitivity (46.67% for mNGS and 40.0% for GeneXpert MTB). Further analysis of the combined efficacy of mNGS and GeneXpert MTB showed that the combined test had a sensitivity of 66.67% and a specificity of 100%. mNGS analysis revealed that MTB was detected in 7 out of 15 patients with tuberculous pleural effusions, while non-tuberculous pleural effusions were associated with a diverse range of microbial genera and species. The most frequently detected genera at the microbial genus level in the NTP group were Microbacterium spp. (6/16), Prevotella spp. (5/16), and Campylobacter spp. (5/16). Discussion These findings suggest that mNGS and GeneXpert MTB are useful diagnostic tools for identifying patients with tuberculous pleurisy, and mNGS can provide valuable insights into the microbial profiles of both tuberculous and non-tuberculous pleural effusions.
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Affiliation(s)
- Fengxiang Huang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haoran Wang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruiping Qiao
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiang Peng
- Department of Respiratory and Critical Care Medicine, Chest Hospital of Henan Province, Zhengzhou, China
| | - Chang Zhao
- Department of Respiratory and Critical Care Medicine, Chest Hospital of Henan Province, Zhengzhou, China
| | - Lijun Miao
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Huang C, Huang Y, Wang Z, Lin Y, Li Y, Chen Y, Chen X, Zhang C, Li W, Zhang W, Fang X, Huang Z. Multiplex PCR-based next generation sequencing as a novel, targeted and accurate molecular approach for periprosthetic joint infection diagnosis. Front Microbiol 2023; 14:1181348. [PMID: 37275128 PMCID: PMC10232910 DOI: 10.3389/fmicb.2023.1181348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/27/2023] [Indexed: 06/07/2023] Open
Abstract
Objectives Periprosthetic joint infection (PJI) diagnosis remains challenging, and the identification of the causative microorganism is, by far, the most important aspect. Here, we use multiple PCR-based targeted next-generation sequencing (tNGS) to detect pathogens in PJI. To explore 1. the ability of targeted next-generation sequencing (tNGS) to detect pathogens in PJI; 2. the consistency of tNGS, metagenomic NGS (mNGS), and culture results; and 3. the ability of tNGS to detect drug resistance genes in PJI. Methods PJI was diagnosed according to the Musculoskeletal Infection Society (MSIS) criteria. The microorganisms were detected by culture, mNGS and tNGS to compare the diagnostic effectiveness of the three methods for PJI and to compare their consistency in detecting microorganisms. Drug resistance genes were detected using tNGS. The costs and turnaround times of mNGS and tNGS were compared. Results Forty-three patients with PJI, 21 patients without PJI and 10 negative control cases were included. The culture, tNGS, and mNGS sensitivities for PJI diagnosis were 74.41%, 88.37%, and 93.02%, respectively, with no significant differences. The specificities were 90.48%, 95.24%, and 95.24%, respectively, with no significant differences. tNGS detected drug resistance genes in 37.5% of culture-positive PJIs. tNGS was superior to mNGS for turnaround time (14.5 h vs. 28 h) and cost ($150 vs. $260). Conclusions tNGS can effectively identify PJI pathogens and may provide drug resistance information, while tNGS is superior to mNGS regarding cost and turnaround time. A multidisciplinary, multi-technology based algorithm to diagnose PJI is appropriate. Highlights 298 microorganisms and 86 drug resistance genes were included in the tNGS panel.Diagnostic efficacy of tNGS is not inferior to that of commonly used indicators.tNGS is superior to mNGS in cost and turnaround time.
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Affiliation(s)
- Changyu Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ying Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ziwen Wang
- Fujian Medical University, Fuzhou, China
| | - Yiming Lin
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yongbin Li
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yang Chen
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xiaoqing Chen
- Department of Orthopedic Surgery, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Chaofan Zhang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xinyu Fang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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Niu J, Wang J, Jia P, Zhang M, Wei E. Clinical features and diagnostic value of metagenomic next -generation sequencing in five cases of non-HIV related Pneumocystis jirovecii pneumonia in children. Front Cell Infect Microbiol 2023; 13:1132472. [PMID: 37009508 PMCID: PMC10060869 DOI: 10.3389/fcimb.2023.1132472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
BackgroundPneumocystis jirovecii (PJ) is an opportunistic pathogenic fungus, and PJ pneumonia (PJP) is a commonly problem in HIV-positive patients. While PJP is not caused by HIV, it generally advances rapidly and can quickly lead to severe respiratory failure. To improve pediatricians’ understanding of the condition and aid early accurate diagnoses and therapy, we examined the clinical characteristics of five instances of non-HIV related PJP (NH-PJP) in children and the efficacy of metagenomic next-generation sequencing (mNGS) in its diagnosis.MethodsFrom January 2020 to June 2022, five children with NH-PJP were admitted to the PICU of the First Affiliated Hospital of Zhengzhou University. We retrospectively summarize the clinical presentation, previous histories, routine laboratory findings, treatment, outcome of regression, and results of mNGS in these five children.ResultsFive male children between the ages of 11 months and 14 years had an acute onset on NH-PJP, three of the children had chest tightness after activity, shortness of breath and paroxysmal dry cough, — and two had high fever and dry cough. All five of the children had several flocculent high-density pictures in both lungs at the beginning of the disease, and lung auscultation revealed coarse breath sounds in both lungs, one of which was accompanied by a modest quantity of dry rales. PJ nuclear sequences were found in one patient and four patients’ blood and alveolar lavage fluid. All five children were treated with Trimethoprim-sulfamethoxazole (TMP-SMX) in combination with Caspofungin and corresponding symptomatic treatment. Four patients were cured and one patient died.ConclusionChildren commonly encounter an initial exposure to NH-PJP, which manifests as a high fever, dry cough, chest discomfort, dyspnea that worsens over time, fast disease progression, and a high death rate. The clinical presentation of children with PJ infection should be taken into consideration along with the results for diagnose. mNGS has higher sensitivity and a shorter detection period compared to identification of PJP.
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Almas S, Carpenter RE, Singh A, Rowan C, Tamrakar VK, Sharma R. Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential. Adv Respir Med 2023; 91:49-65. [PMID: 36825940 PMCID: PMC9952210 DOI: 10.3390/arm91010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Although it is clinically important for acute respiratory tract (co)infections to have a rapid and accurate diagnosis, it is critical that respiratory medicine understands the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n = 29) with a commercially available PCR assay and compared the results with those of a hybridization-capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct < 35 and for mNGS samples it was >40% target coverage, median depth of 1X and RPKM > 10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positively 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterized the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify® Platform (Illumina® Inc, San Diego, CA, USA) for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompromised or immunocompetent with comorbidity respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndrome-based tests, and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration-with promise to reduce morbidity and mortality.
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Affiliation(s)
- Sadia Almas
- Department of Research, Advanta Genetics, 10935 CR 159, Tyler, TX 75703, USA
| | - Rob E. Carpenter
- Department of Research, Advanta Genetics, 10935 CR 159, Tyler, TX 75703, USA
- Department of Human Resource Development, University of Texas at Tyler, 3900 University Boulevard, Tyler, TX 75799, USA
- Correspondence: ; Tel.: +1-903-530-1700
| | - Anuradha Singh
- ICMR-National Institute of Research in Tribal Health, Jabalpur 482003, India
| | - Chase Rowan
- Department of Research, Advanta Genetics, 10935 CR 159, Tyler, TX 75703, USA
| | - Vaibhav K. Tamrakar
- ICMR-National Institute of Research in Tribal Health, Jabalpur 482003, India
- RetroBioTech LLC, 838 Dalmalley Ln, Coppell, TX 75019, USA
| | - Rahul Sharma
- Department of Research, Advanta Genetics, 10935 CR 159, Tyler, TX 75703, USA
- ICMR-National Institute of Research in Tribal Health, Jabalpur 482003, India
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Zhu L, Hao Y, Li W, Shi B, Dong H, Gao P. Significance of pleural effusion detected by metagenomic next-generation sequencing in the diagnosis of aspiration pneumonia. Front Cell Infect Microbiol 2022; 12:992352. [PMID: 36605125 PMCID: PMC9808782 DOI: 10.3389/fcimb.2022.992352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Objective Using metagenomic next-generation sequencing (mNGS) to profile the bacterial pathogen of pleural infection in aspiration pneumonia for therapeutic decision-making. Methods Collection and analysis of the clinical and laboratory data of aspiration pneumonia patients who underwent mNGS detection of pleural effusion at the Second Hospital of Jilin University from November 2020 and March 2022. Results Nine males and one female were included, aged 33 to 69 years. All patients had chest pain, fever, cough, and hypoxemia symptoms; 90% had expectoration. The laboratory tests revealed that all patients had elevated white blood cell, neutrophil, and C-reactive protein (CRP) levels. Furthermore, erythrocyte sedimentation rate (ESR) increased in 8 patients, and procalcitonin increased in only one patient. Chest CT indicated different degrees of lobar pneumonia and pleural effusion in all patients, and biochemical results implied exudative effusion according to Light criteria. Most routine culture results were negative. Among bacteria identified by mNGS, Fusobacterium nucleatum (n=9) was the most common, followed by Parvimonas micra (n=7) and Filifactor alocis (n=6). Three patients underwent surgical treatment after applying targeted antibiotics, thoracic puncture and drainage, and fibrinolytic septum treatment. After the adjusted treatment, the number of white blood cells, neutrophils, and lymphocytes decreased significantly, indicating the eradication of the infection. Conclusions Improving the vigilance of atypical people suffering from aspiration pneumonia is essential. The mNGS detection of pleural effusion clarified the microbial spectrum of aspiration pneumonia, allowing targeted antibiotic administration.
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Zhang B, Gui R, Wang Q, Jiao X, Li Z, Wang J, Han L, Zhou L, Wang H, Wang X, Fan X, Lyu X, Song Y, Zhou J. Comparing the application of mNGS after combined pneumonia in hematologic patients receiving hematopoietic stem cell transplantation and chemotherapy: A retrospective analysis. Front Cell Infect Microbiol 2022; 12:969126. [PMID: 36211959 PMCID: PMC9532739 DOI: 10.3389/fcimb.2022.969126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Rapid and accurate pathogen identification is essential for timely and effective treatment of pneumonia. Here, we describe the use of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BALF) fluid to identify pathogens in patients with hematologic comorbid respiratory symptoms in a retrospective study with 84 patients. In the transplantation group, 8 cases (19.5%) and 47 cases (97.9%) were positive for BALF by conventional method detection and mNGS detection, respectively, and 6 cases (14.0%) and 41 cases (91.1%) in chemotherapy group, respectively. The detection rate of mNGS in both groups was significantly higher than that of conventional detection methods (all P<0.05). Pseudomonas aeruginosa and Streptococcus pneumoniae were the most common bacterial infections in the transplantation and chemotherapy groups, respectively. Aspergillus was the most common fungal infection in both groups. Human betaherpesvirus 5 (HHV-5), torque teno virus and human betaherpesvirus 7 (HHV-7) were the most common pathogen species in both groups. The most common type of infection in patients in the transplantation and chemotherapy groups was the mixed infection of bacteria-virus. Most patients in the transplantation group had mixed infections based on multiple viruses, with 42 cases of viral infections in the transplantation group and 30 cases of viral infections in the chemotherapy group, which were significantly higher in the transplantation group than in the chemotherapy group (χ2 = 5.766, P=0.016). and the mixed infection of virus-virus in the transplantation group was significantly higher than that in the chemotherapy group (27.1% vs 4.4%, P=0.003). The proportion of death due to pulmonary infection was significantly higher in the transplantation group than in the chemotherapy group (76.9% vs 16.7%, χ2 = 9.077, P=0.003). This study demonstrated the value of mNGS of BALF in improving the diagnosis and prognosis of hematologic comorbid pneumonia, helping patients to obtain timely and effective treatment, and giving guidance on the overall treatment plan for patients, with particular benefit for patients with hematologic chemotherapy comorbid pneumonia.
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Affiliation(s)
- Binglei Zhang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- School of Basic Medical Sciences, Academy of Medical Sciences, Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ruirui Gui
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Qian Wang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Xueli Jiao
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Zhen Li
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Juan Wang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Lu Han
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Ling Zhou
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Huili Wang
- Department of Hematology, The Third People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Xianjing Wang
- Department of Hematology, The Third People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Xinxin Fan
- Department of Hematology, The Third People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Xiaodong Lyu
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Xiaodong Lyu, ; Yongping Song, ; Jian Zhou,
| | - Yongping Song
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Xiaodong Lyu, ; Yongping Song, ; Jian Zhou,
| | - Jian Zhou
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Xiaodong Lyu, ; Yongping Song, ; Jian Zhou,
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Shi Y, Peng JM, Qin HY, Du B. Metagenomic next-generation sequencing: A promising tool for diagnosis and treatment of suspected pneumonia in rheumatic patients with acute respiratory failure: Retrospective cohort study. Front Cell Infect Microbiol 2022; 12:941930. [PMID: 35992169 PMCID: PMC9381725 DOI: 10.3389/fcimb.2022.941930] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Background The effectiveness of metagenomic next-generation sequencing (mNGS) in respiratory pathogen detection and clinical decision-making in critically rheumatic patients remains largely unexplored. Methods A single-center retrospective study of 58 rheumatic patients who were admitted to ICU due to suspected pneumonia with acute respiratory failure if they underwent both bronchoalveolar lavage fluid specimen mNGS and combined microbiological tests (CMTs) was conducted to compare their diagnostic performance, using clinical composite diagnosis as the gold standard. Treatment modifications based on mNGS results were also reviewed. Results Forty-three patients were diagnosed with microbiologically confirmed pneumonia and 15 were considered as a non-infectious disease. mNGS outperformed CMTs in the accurate diagnosis of infectious and non-infectious lung infiltration (98.1% [57/58] vs. 87.9% [51/58], P = 0.031). A total of 94 causative pathogens were defined by the gold standard and 27 patients had polymicrobial pneumonia. The sensitivity of pathogen detection and complete concordance with the gold standard by mNGS exceeded those by CMTs (92.6% [87/94] vs. 76.6% [72/94], P < 0.001 and 72.1% [31/43] vs. 51.2% [22/43], P = 0.004, respectively). Moreover, 22 pathogens were detected only by mNGS and confirmed by orthogonal test. Accordingly, the etiological diagnosis changed in 19 cases, and the empirical treatment improved in 14 cases, including 8 cases of rescue treatment and 11 of antibiotics de-escalation. At the pathogen-type level, both methods were comparable for bacteria, but mNGS was advantageous to identify viruses (accuracy: 100% vs. 81%, P = 0.004). For Pneumocystis jirovecii detection, mNGS improved the sensitivity compared with Gomori’s methenamine silver stain (91.7% vs. 4.2%, P < 0.001) and was higher than polymerase chain reaction (79.2%), but the difference was not significant (P = 0.289). In terms of Aspergillus, the better sensitivity with a combination of culture and galactomannan test than that with mNGS was found (100% vs. 66.7%, P = 0.033). Conclusions mNGS has an excellent accuracy in etiological diagnosis and pathogen detection of suspected pneumonia in critically rheumatic patients, which has potential significance for clinical decision-making. Its superiority to different types of pathogens depends on the comprehensiveness of CMTs.
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Su R, Yan H, Li N, Ding T, Li B, Xie Y, Gao C, Li X, Wang C. Application value of blood metagenomic next-generation sequencing in patients with connective tissue diseases. Front Immunol 2022; 13:939057. [PMID: 35979346 PMCID: PMC9376218 DOI: 10.3389/fimmu.2022.939057] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 12/05/2022] Open
Abstract
Objective This study aimed to analyze the application value of blood metagenomic next-generation sequencing (mNGS) in patients with connective tissue diseases (CTDs) to provide a reference for infection diagnosis and guidance for treatment. Methods A total of 126 CTD patients with suspected infections who were hospitalized in the Department of Rheumatology, the Second Hospital of Shanxi Medical University from January 2020 to December 2021 were enrolled in this study. We retrospectively reviewed the results of mNGS and conventional diagnostic tests (CDTs). Results Systemic lupus erythematosus (SLE) and polymyositis/dermatomyositis (DM/PM) had the highest incidence of infections. The positive pathogen detection rates of mNGS were higher than those of CDT. The virus infections are the most common type in CTD patients with single or mixed infection, especially Human gammaherpesvirus 4 (EBV), Human betaherpesvirus 5 (CMV), and Human alphaherpesvirus 1. The incidence of prokaryote and eukaryote infections is secondary to viruses. Bloodstream infections of rare pathogens such as Pneumocystis jirovecii should be of concern. Meanwhile, the most common mixed infection was bacterial–virus coinfection. Conclusion mNGS has incremental application value in patients with CTD suspected of co-infection. It has a high sensitivity, and a wide detection range for microorganisms in CTD patients. Furthermore, the high incidence of opportunistic virus infections in CTD patients should be of sufficient concern.
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Affiliation(s)
- Rui Su
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Huanhuan Yan
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Na Li
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Tingting Ding
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Baochen Li
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuhuan Xie
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Chong Gao
- Pathology, Joint Program in Transfusion Medicine, Brigham and Women’s Hospital/Children’s Hospital Boston, Harvard Medical School, Boston, MA, United States
| | - Xiaofeng Li
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Caihong Wang
- Department of Rheumatology, the Second Hospital of Shanxi Medical University, Taiyuan, China
- *Correspondence: Caihong Wang,
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12
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Zhang X, Li Y, Yin J, Xi B, Wang N, Zhang Y. Application of Next-Generation Sequencing in Infections After Allogeneic Haematopoietic Stem Cell Transplantation: A Retrospective Study. Front Cell Infect Microbiol 2022; 12:888398. [PMID: 35774403 PMCID: PMC9239075 DOI: 10.3389/fcimb.2022.888398] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
This retrospective study aimed to determine the characteristics of infection and diagnostic efficacy of next-generation sequencing (NGS) in patients with fever after allogeneic hematopoietic stem cell transplantation (allo-HSCT). A total of 71 patients with fever after HSCT were enrolled in this study. Compared with conventional microbiological test (CMT), we found that the sensitivity of NGS versus CMT in peripheral blood samples was 91.2% vs. 41.2%, and that NGS required significantly less time to identify the pathogens in both monomicrobial infections (P=0.0185) and polymicrobial infections (P= 0.0027). The diagnostic performance of NGS was not affected by immunosuppressant use. Viruses are the most common pathogens associated with infections. These results indicated that the sensitivity, timeliness, and clinical significance of NGS are superior for the detection of infections. Although NGS has the advantage of identifying a wide range of potential pathogens, the positive rate is related closely to the sample type. Therefore, we recommend that, in the clinical application of NGS to detect pathogens in patients after allo-HSCT, an appropriate sample type and time should be selected and submitted to improve the positive rate and accuracy of NGS. NGS holds promise as a powerful technology for the diagnosis of fever after HSCT.
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Affiliation(s)
- Xiaoying Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jin Yin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bixin Xi
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Na Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yicheng Zhang, ; Na Wang,
| | - Yicheng Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yicheng Zhang, ; Na Wang,
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