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Cai S, Yuan J, Li Y, Guo F, Lin Z, Li H, Miao Q, Fang T, Wu Y, Gao X, Li P, Liu J, Hu C, Hu B. Etiological diagnostic performance of probe capture-based targeted next-generation sequencing in bloodstream infection. J Thorac Dis 2024; 16:2539-2549. [PMID: 38738241 PMCID: PMC11087619 DOI: 10.21037/jtd-24-400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 04/03/2024] [Indexed: 05/14/2024]
Abstract
Background A rapid and precise etiological diagnosis is crucial for the effective treatment of bloodstream infection (BSI). In this study, the performance of probe capture-based targeted next-generation sequencing (tNGS) was compared to that of blood culture and metagenomic next-generation sequencing (mNGS) in detecting potential pathogens in patients with BSI. Methods A total of 80 patients with suspected BSI were prospectively enrolled from 24 November 2023 to 30 December 2023 at Zhongshan Hospital, Shanghai, China. All 80 participants underwent simultaneous blood culture, blood mNGS, and blood tNGS after admission when febrile, and the results were compared. Results Among the 80 participants, 11 were clinically diagnosed with noninfectious fever, and 69 were diagnosed with BSI. Blood tNGS had a higher sensitivity for the diagnosis of BSI than blood culture (91.3% vs. 23.2%, P<0.001) and blood mNGS (91.3% vs. 69.6%, P=0.001). There was no significant difference in specificity between blood mNGS and tNGS (81.8% vs. 100.0%, P=0.13). Blood tNGS demonstrated a faster turnaround time than blood culture and blood mNGS. In 22 (31.9%) patients with BSI, targeted adjustment of the anti-infectious therapy according to the blood tNGS results resulted in clinical improvement. Conclusions Blood tNGS may be a promising tool for detecting potential pathogens in patients with BSI. The application of blood tNGS for BSI could guide anti-infectious treatment strategies and might improve clinical outcomes.
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Affiliation(s)
- Sishi Cai
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianying Yuan
- Guangzhou KingCreate Biotechnology Company Limited, Guangzhou, China
| | - Yingzhen Li
- Guangzhou KingCreate Biotechnology Company Limited, Guangzhou, China
| | - Fengming Guo
- Guangzhou KingCreate Biotechnology Company Limited, Guangzhou, China
| | - Zengshun Lin
- Guangzhou KingCreate Biotechnology Company Limited, Guangzhou, China
| | - Hongyi Li
- Guangzhou KingCreate Biotechnology Company Limited, Guangzhou, China
| | - Qing Miao
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tingting Fang
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuan Wu
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Gao
- Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Pei Li
- Guangzhou KingMed Diagnostics Group Company Limited, Guangzhou, China
| | - Jun Liu
- Guangzhou KingCreate Biotechnology Company Limited, Guangzhou, China
| | - Chaohui Hu
- Guangzhou KingCreate Biotechnology Company Limited, Guangzhou, China
| | - Bijie Hu
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
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Zheng H, Na H, Yao J, Su S, Han F, Li X, Chen X. 16S rRNA seq-identified Corynebacterium promotes pyroptosis to aggravate diabetic foot ulcer. BMC Infect Dis 2024; 24:366. [PMID: 38561650 PMCID: PMC10986075 DOI: 10.1186/s12879-024-09235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Diabetic foot ulcer (DFU) is one of the main chronic complications caused by diabetes, leading to amputation in severe cases. Bacterial infection affects the wound healing in DFU. METHODS DFU patients who met the criteria were selected, and the clinical data were recorded in detail. The pus exudate from the patient's foot wound and venous blood were collected for biochemical analysis. The distribution of bacterial flora in pus exudates of patients was analyzed by 16S rRNA sequencing, and the correlation between DFU and pathogenic variables, pyroptosis and immunity was analyzed by statistical analysis. Then, the effects of key bacteria on the inflammation, proliferation, apoptosis, and pyroptosis of polymorphonuclear leukocytes were investigated by ELISA, CCK-8, flow cytometry, RT-qPCR and western blot. RESULTS Clinical data analysis showed that Wagner score was positively correlated with the level of inflammatory factors, and there was high CD3+, CD4+, and low CD8+ levels in DFU patients with high Wagner score. Through alpha, beta diversity analysis and species composition analysis, Corynebacterium accounted for a large proportion in DFU. Logistics regression model and Person correlation analysis demonstrated that mixed bacterial infections could aggravate foot ulcer, and the number of bacteria was closely related to inflammatory factors PCT, PRT, immune cells CD8+, and pyroptosis-related proteins GSDMD and NLRP3. Through in vitro experiments, Corynebacterium inhibited cell proliferation, promoted inflammation (TNF-α, PCT, CRP), apoptosis and pyroptosis (IL-1β, LDH, IL-18, GSDMD, NLRP3, and caspase-3). CONCLUSION Mixed bacterial infections exacerbate DFU progression with a high predominance of Corynebacterium, and Corynebacterium promotes inflammation, apoptosis and pyroptosis to inhibit DFU healing.
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Affiliation(s)
- Hailong Zheng
- Department of Endocrinology, The First Affiliated Hospital of Hainan Medical University, Hainan Province, No. 31, Longhua Road, Haikou City, 570102, China
| | - Han Na
- Department of Endocrinology, The First Affiliated Hospital of Hainan Medical University, Hainan Province, No. 31, Longhua Road, Haikou City, 570102, China
| | - Jiangling Yao
- Department of Wound Repair, The First Affiliated Hospital of Hainan Medical University, Hainan Province, No. 31, Longhua Road, Haikou City, 570102, China
| | - Sheng Su
- Department of Endocrinology, The First Affiliated Hospital of Hainan Medical University, Hainan Province, No. 31, Longhua Road, Haikou City, 570102, China
| | - Feng Han
- Department of Clinical Laboratory, The First Affiliated Hospital of Hainan Medical University, Hainan Province, No. 31, Longhua Road, Haikou City, 570102, China
| | - Xiaoyan Li
- Department of Endocrinology, The First Affiliated Hospital of Hainan Medical University, Hainan Province, No. 31, Longhua Road, Haikou City, 570102, China
| | - Xiaopan Chen
- Department of Endocrinology, The First Affiliated Hospital of Hainan Medical University, Hainan Province, No. 31, Longhua Road, Haikou City, 570102, China.
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Giedraitiene A, Tatarunas V, Kaminskaite K, Meskauskaite U, Boieva S, Ajima Y, Ciapiene I, Veikutiene A, Zvikas V, Kupstyte-Kristapone N, Jakstas V, Luksiene D, Tamosiunas A, Lesauskaite V. Enterobacterales Biofilm-Specific Genes and Antimicrobial and Anti-Inflammatory Biomarkers in the Blood of Patients with Ischemic Heart Disease. Diagnostics (Basel) 2024; 14:546. [PMID: 38473018 DOI: 10.3390/diagnostics14050546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Ischemic heart disease (IHD) is the most prevalent type of cardiovascular disease. The main cause of IHD is atherosclerosis, which is a multifactorial inflammatory disease of blood vessels. Studies show that bacteria might have a significant impact on the pathogenesis of atherosclerosis and plaque rupture. This study aimed to evaluate the complexity of interactions between bacteria and the human body concerning metabolites and bacterial genes in patients with ischemic heart disease. METHODS Bacterial 16S rDNA and wcaF, papC, and sdhC genes were detected in whole blood using a real-time PCR methodology. An enzyme-linked immunosorbent assay was used to measure the concentration of the LL-37 protein. An analysis of ARA in blood plasma was performed. RESULTS Bacterial 16S rDNA was detected in 31% of the study patients, and the genes wcaF and sdhC in 20%. Enterobacterales genes were detected more frequently in patients younger than 65 years than in patients aged 65 years and older (p = 0.018) and in patients with type 2 diabetes (p = 0.048). Concentrations of the human antimicrobial peptide LL-37 and 12S-HETE concentrations were determined to be higher if patients had 16S rDNA and biofilm-specific genes. CONCLUSIONS The results of this study enhance the understanding that Enterobacterales bacteria may participate in the pathogenesis of atherosclerosis and IHD. Bacterial DNA and host metabolites in higher concentrations appear to be detected.
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Affiliation(s)
- Agne Giedraitiene
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Eiveniu 4, LT 50161 Kaunas, Lithuania
| | - Vacis Tatarunas
- Institute of Cardiology, Lithuanian University of Health Sciences, Sukileliu 15, LT 50103 Kaunas, Lithuania
| | - Kornelija Kaminskaite
- Medical Academy, Lithuanian University of Health Sciences, A. Mickeviciaus 9, LT 44307 Kaunas, Lithuania
| | - Ugne Meskauskaite
- Medical Academy, Lithuanian University of Health Sciences, A. Mickeviciaus 9, LT 44307 Kaunas, Lithuania
| | - Svitlana Boieva
- Institute of Cardiology, Lithuanian University of Health Sciences, Sukileliu 15, LT 50103 Kaunas, Lithuania
| | - Yu Ajima
- Medical Academy, Lithuanian University of Health Sciences, A. Mickeviciaus 9, LT 44307 Kaunas, Lithuania
- School of Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Ieva Ciapiene
- Institute of Cardiology, Lithuanian University of Health Sciences, Sukileliu 15, LT 50103 Kaunas, Lithuania
| | - Audrone Veikutiene
- Institute of Cardiology, Lithuanian University of Health Sciences, Sukileliu 15, LT 50103 Kaunas, Lithuania
| | - Vaidotas Zvikas
- Institute of Pharmaceutical Technologies, Lithuanian University of Health Sciences, Sukileliu 13, LT 50161 Kaunas, Lithuania
| | - Nora Kupstyte-Kristapone
- Medical Academy, Lithuanian University of Health Sciences, A. Mickeviciaus 9, LT 44307 Kaunas, Lithuania
| | - Valdas Jakstas
- Institute of Pharmaceutical Technologies, Lithuanian University of Health Sciences, Sukileliu 13, LT 50161 Kaunas, Lithuania
| | - Dalia Luksiene
- Institute of Cardiology, Lithuanian University of Health Sciences, Sukileliu 15, LT 50103 Kaunas, Lithuania
| | - Abdonas Tamosiunas
- Institute of Cardiology, Lithuanian University of Health Sciences, Sukileliu 15, LT 50103 Kaunas, Lithuania
| | - Vaiva Lesauskaite
- Institute of Cardiology, Lithuanian University of Health Sciences, Sukileliu 15, LT 50103 Kaunas, Lithuania
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Kuruwa S, Zade A, Shah S, Moidu R, Lad S, Chande C, Joshi A, Hirani N, Nikam C, Bhattacharya S, Poojary A, Kapoor M, Kondabagil K, Chatterjee A. An integrated method for targeted Oxford Nanopore sequencing and automated bioinformatics for the simultaneous detection of bacteria, fungi, and ARG. J Appl Microbiol 2024; 135:lxae037. [PMID: 38346849 DOI: 10.1093/jambio/lxae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
AIMS The use of metagenomics for pathogen identification in clinical practice has been limited. Here we describe a workflow to encourage the clinical utility and potential of NGS for the screening of bacteria, fungi, and antimicrobial resistance genes (ARGs). METHODS AND RESULTS The method includes target enrichment, long-read sequencing, and automated bioinformatics. Evaluation of several tools and databases was undertaken across standard organisms (n = 12), clinical isolates (n = 114), and blood samples from patients with suspected bloodstream infections (n = 33). The strategy used could offset the presence of host background DNA, error rates of long-read sequencing, and provide accurate and reproducible detection of pathogens. Eleven targets could be successfully tested in a single assay. Organisms could be confidently identified considering ≥60% of best hits of a BLAST-based threshold of e-value 0.001 and a percent identity of >80%. For ARGs, reads with percent identity of >90% and >60% overlap of the complete gene could be confidently annotated. A kappa of 0.83 was observed compared to standard diagnostic methods. Thus, a workflow for the direct-from-sample, on-site sequencing combined with automated genomics was demonstrated to be reproducible. CONCLUSION NGS-based technologies overcome several limitations of current day diagnostics. Highly sensitive and comprehensive methods of pathogen screening are the need of the hour. We developed a framework for reliable, on-site, screening of pathogens.
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Affiliation(s)
- Sanjana Kuruwa
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Amrutraj Zade
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanchi Shah
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rameez Moidu
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shailesh Lad
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chhaya Chande
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Ameeta Joshi
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Nilma Hirani
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Chaitali Nikam
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- Thyrocare Technologies Pvt. Ltd, Navi Mumbai 400703, India
| | - Sanjay Bhattacharya
- Department of Microbiology, Tata Medical Center, 14, MAR(E-W), DH Block (Newtown), Action Area I, Newtown, Kolkata, Chakpachuria 700160, India
| | - Aruna Poojary
- Department of Microbiology, Breach Candy Hospital and Research Center, Mumbai 400026, India
| | - Mahua Kapoor
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Kiran Kondabagil
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anirvan Chatterjee
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Yu J, Zhang L, Gao D, Wang J, Li Y, Sun N. Comparison of metagenomic next-generation sequencing and blood culture for diagnosis of bloodstream infections. Front Cell Infect Microbiol 2024; 14:1338861. [PMID: 38328669 PMCID: PMC10847245 DOI: 10.3389/fcimb.2024.1338861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
Objectives This study aimed to evaluate the clinical performance of plasma cell-free DNA (cfDNA) next-generation sequencing (NGS) for pathogen detection in patients with sepsis. Methods A total of 43 pairs of blood and plasma samples form 33 blood culture-positive patients were used as testing samples in metagenomic NGS (mNGS) and NGS of 16S ribosomal RNA gene amplicons (16S rRNA NGS). The results of routine tests, including microbial culture, complete blood count, and biochemical tests, were collected from electronic medical records. Results Using blood as an mNGS testing sample, the proportion of host DNA was 99.9%, with only three bacteria and no fungi detected. When using plasma in mNGS, the proportion of host DNA was approximately 97%, with 84 bacteria and two fungi detected. Notably, 16S rRNA NGS detected 15 and 16 bacteria in 43 pairs of blood and plasma samples, respectively. Blood culture detected 49 bacteria (23 gram-negative bacilli and 26 gram-positive cocci) and four fungi, with 14 bacteria considered contaminants by clinical microbiologists. For all blood cultures, plasma cfDNA mNGS detected 78.26% (19/23) gram-negative rods, 17% (2/12) gram-positive cocci, and no fungi. Compared to blood cultures, the sensitivity and specificity of plasma cfDNA mNGS for detecting bacteria and fungi were 62.07% and 57.14%, respectively. Conclusion Compared to blood, plasma is more suitable for the detection of bloodstream infections using mNGS and is less affected by host DNA. The positive detection rate of plasma cfDNA mNGS for bloodstream infections caused by gram-negative bacteria was higher than that caused by gram-positive cocci.
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Affiliation(s)
- Juan Yu
- Department of Clinical Laboratory, Nanjing Lishui People’s Hospital, Nanjing, China
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Li Zhang
- Department of Clinical Laboratory, Nanjing Lishui People’s Hospital, Nanjing, China
| | - Deyu Gao
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jie Wang
- Clinical Medicine Research Center, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, China
| | - Yi Li
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Ning Sun
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
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Sumiyoshi S, Aoki K, Motobayashi H, Yogo A, Tochitani K. Contamination rate of rare bacterial species detected by MALDI-TOFMS: a retrospective cohort study. Diagn Microbiol Infect Dis 2024; 108:116110. [PMID: 37924747 DOI: 10.1016/j.diagmicrobio.2023.116110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 11/06/2023]
Abstract
When rare bacterial species are identified in blood cultures, determining the clinical significance is sometimes difficult. This study aimed to analyze the clinical significance of rare bacterial species detected in blood cultures using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOFMS) by comparing their contamination rates with those of common species. We retrospectively analyzed medical records of adult patients with positive blood cultures at Kyoto City Hospital from 2014 to 2022. Rare species were defined by low detection rates and few PubMed reports. Of 4880 microorganisms identified from 3441 individuals, 1150 (23.6%) were classified as contamination. Meanwhile, 24 rare microorganisms were identified, of which 14 (58.3%) were classified as contamination, which was significantly higher than common species (odds ratio 4.56, 95% confidence Interval 1.88-11.50, P < 0.001). These findings may help in determining the clinical significance of rare bacterial species in blood cultures with few reported cases.
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Affiliation(s)
- Shougen Sumiyoshi
- Department of Infection Control and Prevention, Osaka University, Osaka, Japan.
| | - Kazuaki Aoki
- Department of General Internal Medicine, Kameda Medical Center, Chiba, Japan
| | | | - Aoi Yogo
- Division of Infectious Diseases, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
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Poulsen SH, Søgaard KK, Fuursted K, Nielsen HL. Evaluating the diagnostic accuracy and clinical utility of 16S and 18S rRNA gene targeted next-generation sequencing based on five years of clinical experience. Infect Dis (Lond) 2023; 55:767-775. [PMID: 37535652 DOI: 10.1080/23744235.2023.2241550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND The use of 16S/18S rRNA targeted next-generation sequencing (tNGS) has improved microbial diagnostics, however, the use of tNGS in a routine clinical setting requires further elucidation. We retrospectively evaluated the diagnostic accuracy and clinical utility of 16S/18S tNGS, routinely used in the North Denmark Region between 2017 and 2021. METHODS We retrieved 544 tNGS results from 491 patients hospitalised with suspected infection (e.g. meningitis, pneumonia, intraabdominal abscess, osteomyelitis and joint infection). The tNGS assays was performed using the Illumina MiSeq desktop sequencer, and BION software for annotation. The patients' diagnosis and clinical management was evaluated by medical chart review. We calculated sensitivity and specificity, and determined the diagnostic accuracy of tNGS by defining results as true positive, true negative, false positive, and false negative. RESULTS Overall, tNGS had a sensitivity of 56% and a specificity of 97%. tNGS was more frequently true positive compared to culture (32% vs 18%), and tNGS detected a greater variety of bacteria and fungi, and was more frequently polymicrobial. However, the total diagnostic turnaround time was 16 days, and although 73% of tNGS results were true positive or true negative, only 4.4% of results led to changes in clinical management. CONCLUSIONS As a supplement to culture, tNGS improves identification of pathogenic microorganisms in a broad range of clinical specimens. However, the long turnaround time of tNGS in our setting may have contributed to a limited clinical utility. An improved turnaround time can be the key to improved clinical utility in a future setting.
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Affiliation(s)
| | - Kirstine Kobberøe Søgaard
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Hans Linde Nielsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
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Yuan Q, Mao D, Tang X, Liu C, Zhang R, Deng J, Zhu X, Li W, Man Q, Sun F. Biological effect abundance analysis of hemolytic pathogens based on engineered biomimetic sensor. Biosens Bioelectron 2023; 237:115502. [PMID: 37423067 DOI: 10.1016/j.bios.2023.115502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/11/2023]
Abstract
Conventional pathogen detection strategies based on the molecular structure or chemical characteristics of biomarkers can only provide the "physical abundance" of microorganisms, but cannot reflect the "biological effect abundance" in the true sense. To address this issue, we report an erythrocyte membrane-encapsulated biomimetic sensor cascaded with CRISPR-Cas12a (EMSCC). Taking hemolytic pathogens as the target model, we first constructed an erythrocyte membrane-encapsulated biomimetic sensor (EMS). Only hemolytic pathogens with biological effects can disrupt the erythrocyte membrane (EM), resulting in signal generation. Then the signal was amplified by cascading CRISPR-Cas12a, and more than 6.67 × 104-fold improvement in detection sensitivity compared to traditional erythrocyte hemolysis assay was achieved. Notably, compared with polymerase chain reaction (PCR) or enzyme linked immunosorbent assay (ELISA)-based quantification methods, EMSCC can sensitively respond to the pathogenicity change of pathogens. For the detection of simulated clinical samples based on EMSCC, we obtained an accuracy of 95% in 40 samples, demonstrating its potential clinical value.
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Affiliation(s)
- Qianqin Yuan
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, PR China
| | - Dongsheng Mao
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, PR China
| | - Xiaochen Tang
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China; Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, PR China
| | - Chenbin Liu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, PR China
| | - Runchi Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, PR China
| | - Jie Deng
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, PR China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, PR China
| | - Wenxing Li
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, PR China.
| | - Qiuhong Man
- Department of Clinical Laboratory Medicine, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200080, PR China.
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, PR China.
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Sun N, Chen Y, Zhang J, Cao J, Huang H, Wang J, Guo W, Li X. Identification and characterization of pancreatic infections in severe and critical acute pancreatitis patients using 16S rRNA gene next generation sequencing. Front Microbiol 2023; 14:1185216. [PMID: 37389346 PMCID: PMC10303115 DOI: 10.3389/fmicb.2023.1185216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023] Open
Abstract
Objectives This study aimed to identify the bacterial composition in the pancreatic fluid of severe and critical acute pancreatitis (SAP and CAP) patients. Methods A total of 78 pancreatic fluid samples were collected from 56 SAP and CAP patients and analyze using aerobic culture and 16S rRNA gene next-generation sequencing. The clinical data of the patients were obtained from the electronic medical records. Results Among the total 78 samples, 16S rRNA gene NGS identified a total of 660 bacterial taxa, belonging to 216 species in 123 genera. The dominant aerobic bacteria included Klebsiella pneumoniae, Acinetobacter baumannii, and Enterococcus faecium, while the dominant anaerobic bacteria included Bacteroides, Dialister invisus, and Olsenella uli. As compared to aerobic culturing, 95.96% (95/99) of the aerobic cultured bacteria were detected using the 16S rRNA gene NGS. Conclusion The pancreatic infections in SAP and CAP patients might originate not only from the gut but also from the oral cavity and airways as well as related environments. Dynamic analysis of bacterial profile and abundance showed that some bacteria with low abundance might become the main pathogenic bacteria. There were no significant differences in the bacterial diversity between SAP and CAP.
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Affiliation(s)
- Ning Sun
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yong Chen
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jiaxun Zhang
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jin Cao
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Hongjuan Huang
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jie Wang
- Clinical Medicine Research Center, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, China
| | - Wentao Guo
- Department of Microbiology and Immunology, College of Basic Medicine, Guangdong Medical University, Dongguan, China
| | - Xiaojun Li
- Department of Clinical Laboratory Science, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
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10
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Everhart J, Henshaw NG. Updates in Molecular Diagnostics in Solid Organ Transplantation Recipients. Infect Dis Clin North Am 2023:S0891-5520(23)00038-7. [PMID: 37244805 DOI: 10.1016/j.idc.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Advances in molecular diagnostics have the potential to improve patient care among solid organ transplant recipients by reducing time to pathogen identification and informing directed therapy. Although cultures remain the cornerstone of traditional microbiology, advanced molecular diagnostics, such as metagenomic next-generation sequencing (mNGS), may increase detection of pathogens. This is particularly true in the settings of prior antibiotic exposure, and when causative organisms are fastidious. mNGS also offers a hypothesis-free diagnostic method of testing. This is useful in situations whereby the differential is broad or when the infectious agent is unlikely to be detected by routine methods.
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Affiliation(s)
- James Everhart
- Duke University Medical Center, 2351 Erwin Road, Wadsworth Building, Room 0170, Durham, NC 27705, USA.
| | - Nancy G Henshaw
- Duke University Medical Center, 2351 Erwin Road, Wadsworth Building, Room 0170, Durham, NC 27705, USA
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11
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Alves J, Abreu B, Palma P, Alp E, Vieceli T, Rello J. Antimicrobial Stewardship on Patients with Neutropenia: A Narrative Review Commissioned by Microorganisms. Microorganisms 2023; 11:1127. [PMID: 37317101 DOI: 10.3390/microorganisms11051127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 06/16/2023] Open
Abstract
The emergence of antibiotic resistance poses a global health threat. High-risk patients such as those with neutropenia are particularly vulnerable to opportunistic infections, sepsis, and multidrug-resistant infections, and clinical outcomes remain the primary concern. Antimicrobial stewardship (AMS) programs should mainly focus on optimizing antibiotic use, decreasing adverse effects, and improving patient outcomes. There is a limited number of published studies assessing the impact of AMS programs on patients with neutropenia, where early appropriate antibiotic choice can be the difference between life and death. This narrative review updates the current advances in strategies of AMS for bacterial infections among high-risk patients with neutropenia. Diagnosis, drug, dose, duration, and de-escalation (5D) are the core variables among AMS strategies. Altered volumes of distribution can make standard dose regimens inadequate, and developing skills towards a personalized approach represents a major advance in therapy. Intensivists should partner antibiotic stewardship programs to improve patient care. Assembling multidisciplinary teams with trained and dedicated professionals for AMS is a priority.
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Affiliation(s)
- Joana Alves
- Infectious Diseases Department, Hospital de Braga, 4710-243 Braga, Portugal
| | - Betânia Abreu
- Pharmaceuticals Department, Hospital de Braga, 4710-243 Braga, Portugal
| | - Pedro Palma
- Infectious Diseases Department, Centro Hospitalar do Tâmega e Sousa, 4564-007 Penafiel, Portugal
| | - Emine Alp
- Infectious Diseases and Clinical Microbiology Department, Ankara Yıldırım Beyazıt University, 06760 Ankara, Turkey
| | - Tarsila Vieceli
- Infectious Diseases Department, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, Brazil
| | - Jordi Rello
- Clinical Research in Pneumonia & Sepsis (CRIPS), Vall d'Hebron Institute of Research (VHIR), 08035 Barcelona, Spain
- FOREVA Research Pôle, Centre Hôpitalaire Universitaire de Nîmes, 30900 Nîmes, France
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12
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Rello J, Paiva JA. Antimicrobial stewardship at the emergency department: Dead bugs do not mutate! Eur J Intern Med 2023; 109:30-32. [PMID: 36669904 DOI: 10.1016/j.ejim.2023.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023]
Affiliation(s)
- Jordi Rello
- Clinical Research/Epidemiology in Pneumonia & Sepsis (CRIPS), Vall d'Hebron Research Institute, Barcelona, Spain; Recherche in Pôle Reánimation, Urgences et Douleur, CHU Nîmes, Nîmes, France.
| | - José Artur Paiva
- Intensive Care Department, Centro Hospitalar Universitário Sao Joao, Porto, Portugal; Medicine Departement, Faculty of Medicine, University of Porto, Portugal.
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13
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Hong HL, Flurin L, Thoendel MJ, Wolf MJ, Abdel MP, Greenwood-Quaintance KE, Patel R. Targeted Versus Shotgun Metagenomic Sequencing-based Detection of Microorganisms in Sonicate Fluid for Periprosthetic Joint Infection Diagnosis. Clin Infect Dis 2023; 76:e1456-e1462. [PMID: 35944127 PMCID: PMC10169413 DOI: 10.1093/cid/ciac646] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/15/2022] [Accepted: 08/08/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is increasingly used for periprosthetic joint infection (PJI) diagnosis, but its clinical utility is poorly defined. Shotgun metagenomic sequencing (sNGS) has been reported to identify PJI pathogens undetected by culture in sonicate fluid. However, sNGS is complex and costly. Here, 16S ribosomal RNA (rRNA) gene-based targeted metagenomic sequencing (tNGS) was compared to sNGS of sonicate fluid for microbial detection and identification in patients with total hip arthroplasty (THA) and total knee arthroplasty (TKA) failure. METHODS A convenience sample of sonicate fluids derived from patients who had undergone THA or TKA removal, enriched with culture negative PJI cases, was tested. Samples had been previously tested by sNGS. For tNGS, samples were extracted, amplified by polymerase chain reaction targeting the V1 to V3 regions of the 16S rRNA gene, and sequenced on an Illumina MiSeq. RESULTS A total of 395 sonicate fluids, including 208 from subjects with PJI, were studied. Compared with sonicate fluid culture, tNGS had higher positive percent agreement (72.1 vs 52.9%, P < .001), detecting potential pathogens in 48.0% of culture-negative PJIs. There was no difference between the positive percent agreement of tNGS (72.1%) and sNGS (73.1%, P = .83). CONCLUSIONS 16S rRNA gene-based tNGS is a potential diagnostic tool for PJI pathogen identification in sonicate fluid from failed THAs and TKAs in culture-negative cases, with similar performance characteristics to sNGS.
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Affiliation(s)
- Hyo-Lim Hong
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Internal Medicine, Daegu Catholic University School of Medicine, Daegu, Republic of Korea
| | - Laure Flurin
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Intensive Care, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Matthew J Thoendel
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J Wolf
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Kerryl E Greenwood-Quaintance
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
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14
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Maeda Y, Murakami T. Diagnosis by Microbial Culture, Breath Tests and Urinary Excretion Tests, and Treatments of Small Intestinal Bacterial Overgrowth. Antibiotics (Basel) 2023; 12:antibiotics12020263. [PMID: 36830173 PMCID: PMC9952535 DOI: 10.3390/antibiotics12020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
Small intestinal bacterial overgrowth (SIBO) is characterized as the increase in the number and/or alteration in the type of bacteria in the upper gastrointestinal tract and accompanies various bowel symptoms such as abdominal pain, bloating, gases, diarrhea, and so on. Clinically, SIBO is diagnosed by microbial culture in duodenum/jejunum fluid aspirates and/or the breath tests (BT) of hydrogen/methane gases after ingestion of carbohydrates such as glucose. The cultural analysis of aspirates is regarded as the golden standard for the diagnosis of SIBO; however, this is invasive and is not without risk to the patients. BT is an inexpensive and safe diagnostic test but lacks diagnostic sensitivity and specificity depending on the disease states of patients. Additionally, the urinary excretion tests are used for the SIBO diagnosis using chemically synthesized bile acid conjugates such as cholic acid (CA) conjugated with para-aminobenzoic acid (PABA-CA), ursodeoxycholic acid (UDCA) conjugated with PABA (PABA-UDCA) or conjugated with 5-aminosalicylic acid (5-ASA-UDCA). These conjugates are split by bacterial bile acid (cholylglycine) hydrolase. In the tests, the time courses of the urinary excretion rates of PABA or 5-ASA, including their metabolites, are determined as the measure of hydrolytic activity of intestinal bacteria. Although the number of clinical trials with this urinary excretion tests is small, results demonstrated the usefulness of bile acid conjugates as SIBO diagnostic substrates. PABA-UDCA disulfate, a single-pass type unabsorbable compound without the hydrolysis of conjugates, was likely to offer a simple and rapid method for the evaluation of SIBO without the use of radioisotopes or expensive special apparatus. Treatments of SIBO with antibiotics, probiotics, therapeutic diets, herbal medicines, and/or fecal microbiota transplantation are also reviewed.
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Affiliation(s)
- Yorinobu Maeda
- Laboratory of Drug Information Analytics, Faculty of Pharmacy & Pharmaceutical Sciences, Fukuyama University, Sanzou, Gakuen-cho, Fukuyama 729-0292, Hiroshima, Japan
| | - Teruo Murakami
- Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1 Hiro-koshingai, Kure 737-0112, Hiroshima, Japan
- Correspondence: ; Tel.: +81-82-872-4310
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15
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Cai Y, Ding H, Chen X, Chen Y, Huang C, Zhang C, Huang Z, Huang Y, Li W, Zhang W, Fang X. Optimization and standardization of mNGS-based procedures for the diagnosis of Mycoplasma periprosthetic joint infection: A novel diagnostic strategy for rare bacterial periprosthetic joint infection. Front Cell Infect Microbiol 2023; 13:1089919. [PMID: 36936762 PMCID: PMC10014592 DOI: 10.3389/fcimb.2023.1089919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/07/2023] [Indexed: 03/05/2023] Open
Abstract
Introduction The diagnosis of Mycoplasma periprosthetic joint infection (PJI) is rather difficult due to its rarity and difficult in isolation, there are not standardized diagnostic procedure for Mycoplasma PJI presently. This study aimed to reported a metagenomic next-generation sequencing (mNGS)-based diagnostic strategy for Mycoplasma PJI. Methods In the present study, we have reported the largest number of Mycoplasma PJI that were precisely diagnosed by mNGS and verified by optimized microbial culture methods and (or) 16S PCR polymerase chain reaction (PCR). Results The positive rate of optimized microbial culture methods and 16S PCR in the detection of Mycoplasma PJI was 57.14% and 71.43%, respectively. The infections were well controlled by targeted treatment in all cases. Conclusion The standardized and optimized procedure based on mNGS presented in this study is useful for the diagnosis of Mycoplasma PJI, which might also be provided as a novel diagnostic strategy for rare bacterial PJI.
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Affiliation(s)
- Yuanqing Cai
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Haiqi Ding
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiaoqing Chen
- Department of Orthopedics, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Yang Chen
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Changyu Huang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Chaofan Zhang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Zida Huang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Ying Huang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenbo Li
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenming Zhang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Wenming Zhang, ; Xinyu Fang,
| | - Xinyu Fang
- Department of Orthopedics, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Department of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- *Correspondence: Wenming Zhang, ; Xinyu Fang,
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Flurin L, Wolf MJ, Fisher CR, Cano Cevallos EJ, Vaillant JJ, Pritt BS, DeSimone DC, Patel R. Pathogen Detection in Infective Endocarditis Using Targeted Metagenomics on Whole Blood and Plasma: a Prospective Pilot Study. J Clin Microbiol 2022; 60:e0062122. [PMID: 36040200 PMCID: PMC9491191 DOI: 10.1128/jcm.00621-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/14/2022] [Indexed: 11/20/2022] Open
Abstract
Initial microbiologic diagnosis of infective endocarditis (IE) relies on blood cultures and Bartonella and Coxiella burnetii serology. Small case series and one prospective study have preliminarily reported application of metagenomic sequencing on blood or plasma for IE diagnosis. Here, results of a prospective pilot study evaluating targeted metagenomic sequencing (tMGS) for blood-based early pathogen detection and identification in IE are reported. Subjects diagnosed with possible or definite IE at a single institution were prospectively enrolled with informed consent from October 2020 to July 2021. Blood was drawn and separated into whole blood and plasma. Both specimen types were subjected to nucleic acid extraction and PCR targeting the V1-V3 region of the 16S ribosomal RNA gene, followed by next-generation sequencing on an Illumina MiSeqTM platform. 35 subjects, 28 (80%) with definite and 7 (20%) with possible IE were enrolled, including 6 (17%) with blood culture-negative endocarditis (BCNE). Overall, 20 whole blood (59%) and 16 plasma (47%) samples tested positive (P = 0.47). When results of whole blood and plasma testing were combined, a positive tMGS result was found in 23 subjects (66%). tMGS identified a potential pathogen in 5 of 6 culture-negative IE cases. Although further study is needed, the results of this pilot study suggest that blood-based tMGS may provide pathogen identification in subjects with IE, including in culture-negative cases.
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Affiliation(s)
- Laure Flurin
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Intensive Care, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Matthew J. Wolf
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Cody R. Fisher
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Edison J. Cano Cevallos
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Memorial Healthcare System, Hollywood, Florida, USA
| | - James J. Vaillant
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S. Pritt
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel C. DeSimone
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
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17
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Purushothaman S, Meola M, Egli A. Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics. Int J Mol Sci 2022; 23:9834. [PMID: 36077231 PMCID: PMC9456280 DOI: 10.3390/ijms23179834] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/21/2022] Open
Abstract
Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.
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18
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West PT, Brooks EF, Costales C, Moreno A, Jensen TD, Budvytiene I, Khan A, Pham THM, Schwenk HT, Bhatt AS, Banaei N. Near-fatal Legionella pneumonia in a neonate linked to home humidifier by metagenomic next generation sequencing. Med 2022; 3:565-567. [PMID: 35863347 PMCID: PMC9769437 DOI: 10.1016/j.medj.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/31/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Patrick T West
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Erin F Brooks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Cristina Costales
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Angel Moreno
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tanner Dean Jensen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Indre Budvytiene
- Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA
| | - Aslam Khan
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Trung H M Pham
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Hayden T Schwenk
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Microbiology Laboratory, Stanford University Medical Center, Palo Alto, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Zhu J, Xia H, Tang R, Ng TK, Yao F, Liao X, Zhang Q, Ke X, Shi T, Chen H. METAGENOMIC NEXT-GENERATION SEQUENCING DETECTS PATHOGENS IN ENDOPHTHALMITIS PATIENTS. Retina 2022; 42:992-1000. [PMID: 35019890 DOI: 10.1097/iae.0000000000003406] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
PURPOSE To investigate the utility of metagenomic next-generation sequencing (mNGS) in identifying the pathogens in endophthalmitis. METHODS In this prospective study, 36 cases of endophthalmitis were recruited. All patients received surgical treatment and intraocular drug lavage. The samples of vitreous or aqueous humor were extracted for mNGS and microbiological culture. The diagnostic performance of pathogens was compared between mNGS and culture. RESULTS The positive rates of mNGS and culture were 88.89% (32/36) and 27.78% (10/36), respectively. There was a statistically significant difference between mNGS and culture (Chi-square = 27.657; P < 0.01). Staphylococcus epidermidis, Streptococcus pneumoniae, and Klebsiella pneumoniae were the most pathogenic bacteria in traumatic, postoperative, and endogenous endophthalmitis, respectively. The concordance of pathogen identified by mNGS and culture was 70% for culture-positive cases. Antibiotic resistance genes were identified in 9 cases. There was a marginal correlation between the final visual acuity and the microbial sequence read (Spearman correlation coefficient = 0.498; P = 0.05). CONCLUSION Metagenomic next-generation sequencing has a higher positive rate of identifying pathogens in endophthalmitis than in culture. It can also provide information on antibiotic resistance and visual prognosis. However, caution must be taken when interpreting the results of mNGS because they may not be concordant with culture.
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Affiliation(s)
- Junfeng Zhu
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Honghe Xia
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Ruqing Tang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Tsz Kin Ng
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Fen Yao
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Xulong Liao
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Qi Zhang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Xixuan Ke
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Tingkun Shi
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Haoyu Chen
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
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20
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Doualeh M, Payne M, Litton E, Raby E, Currie A. Molecular Methodologies for Improved Polymicrobial Sepsis Diagnosis. Int J Mol Sci 2022; 23:ijms23094484. [PMID: 35562877 PMCID: PMC9104822 DOI: 10.3390/ijms23094484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/19/2022] Open
Abstract
Polymicrobial sepsis is associated with worse patient outcomes than monomicrobial sepsis. Routinely used culture-dependent microbiological diagnostic techniques have low sensitivity, often leading to missed identification of all causative organisms. To overcome these limitations, culture-independent methods incorporating advanced molecular technologies have recently been explored. However, contamination, assay inhibition and interference from host DNA are issues that must be addressed before these methods can be relied on for routine clinical use. While the host component of the complex sepsis host–pathogen interplay is well described, less is known about the pathogen’s role, including pathogen–pathogen interactions in polymicrobial sepsis. This review highlights the clinical significance of polymicrobial sepsis and addresses how promising alternative molecular microbiology methods can be improved to detect polymicrobial infections. It also discusses how the application of shotgun metagenomics can be used to uncover pathogen/pathogen interactions in polymicrobial sepsis cases and their potential role in the clinical course of this condition.
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Affiliation(s)
- Mariam Doualeh
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
| | - Matthew Payne
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Division of Obstetrics and Gynaecology, University of Western Australia, Perth, WA 6008, Australia
| | - Edward Litton
- Intensive Care Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Intensive Care Unit, St. John of God Hospital, Subiaco, WA 6009, Australia
| | - Edward Raby
- State Burns Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Microbiology Department, Path West Laboratory Medicine, Murdoch, WA 6150, Australia
| | - Andrew Currie
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Correspondence: ; Tel.: +61-(08)-9360-7426
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Flurin L, Wolf M, Mutchler M, Daniels M, Wengenack N, Patel R. Targeted Metagenomic Sequencing-Based Approach Applied to 2,146 Tissue and Body Fluid Samples in Routine Clinical Practice. Clin Infect Dis 2022; 75:1800-1808. [PMID: 35362534 PMCID: PMC9662179 DOI: 10.1093/cid/ciac247] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The yield of next generation sequencing (NGS) added to a Sanger sequencing-based 16S ribosomal RNA (rRNA) gene PCR assay was evaluated in clinical practice for diagnosis of bacterial infection. METHODS PCR targeting the V1 to V3 regions of the 16S rRNA gene was performed, with amplified DNA submitted to Sanger sequencing and/or NGS (Illumina MiSeq), or reported as negative, depending on cycle threshold (Ct) value. 2,146 normally sterile tissues or body fluids were tested between August 2020 and March 2021. Clinical sensitivity was assessed in 579 subjects from whom clinical data was available. RESULTS Compared to Sanger sequencing alone (400 positive tests), positivity increased by 87% by adding NGS (347 added positive tests). Clinical sensitivity of the assay incorporating NGS was 53%, higher than culture (42%, p<0.001), with an impact on clinical decision-making in 14% of infected cases. Clinical sensitivity in the subgroup receiving antibiotics at sampling was 41% for culture and 63% for the sequencing assay (p<0.001). CONCLUSION Adding NGS to Sanger sequencing of the PCR-amplified 16S rRNA gene substantially improved test positivity. In the patient population studied, the assay was more sensitive than culture, and especially so in patients who had received antibiotic therapy.
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Affiliation(s)
- Laure Flurin
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA.,Department of Intensive Care, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Matthew Wolf
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Melissa Mutchler
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Matthew Daniels
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Nancy Wengenack
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Robin Patel
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA.,Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA
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22
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Li Q, Huang W, Zhang S, Zheng Y, Lv Q, Kong D, Zhang L, Zhang Y, Zhao Z, Wang M, Jiang H, Liu P, Jiang Y. Target-enriched sequencing enables accurate identification of bloodstream infections in whole blood. J Microbiol Methods 2021; 192:106391. [PMID: 34915067 DOI: 10.1016/j.mimet.2021.106391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022]
Abstract
Bloodstream infections are within the top ten causes of death globally, with a mortality rate of up to 70%. Gold standard blood culture testing is time-consuming, resulting in delayed, but accurate, treatment. Molecular methods, such as RT-qPCR, have limited targets in one run. We present a new Ampliseq detection system (ADS) combining target amplification and next-generation sequencing for accurate identification of bacteria, fungi, and antimicrobial resistance determinants directly from blood samples. In this study, we included removal of human genomic DNA during nucleic acid extraction, optimized the target sequence set and drug resistance genes, performed antimicrobial resistance profiling of clinical isolates, and evaluated mock specimens and clinical samples by ADS. ADS successfully identified pathogens at the species-level in 36 h, from nucleic acid extraction to results. Besides pathogen identification, ADS can also present drug resistance profiles. ADS enabled detection of all bacteria and accurate identification of 47 pathogens. In 20 spiked samples and 8 clinical specimens, ADS detected at least 92.81% of reads mapped to pathogens. ADS also showed consistency with the three culture-negative samples, and correctly identified pathogens in four of five culture-positive clinical blood specimens. This Ampliseq-based technology promises broad coverage and accurate pathogen identification, helping clinicians to accurately diagnose and treat bloodstream infections.
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Abstract
INTRODUCTION Rapid and sensitive diagnostic strategies are necessary for patient care and public health. Most of the current conventional microbiological assays detect only a restricted panel of pathogens at a time or require a microbe to be successfully cultured from a sample. Clinical metagenomics next-generation sequencing (mNGS) has the potential to unbiasedly detect all pathogens in a sample, increasing the sensitivity for detection and enabling the discovery of unknown infectious agents. AREAS COVERED High expectations have been built around mNGS; however, this technique is far from widely available. This review highlights the advances and currently available options in terms of costs, turnaround time, sensitivity, specificity, validation, and reproducibility of mNGS as a diagnostic tool in clinical microbiology laboratories. EXPERT OPINION The need for a novel diagnostic tool to increase the sensitivity of microbial diagnostics is clear. mNGS has the potential to revolutionise clinical microbiology. However, its role as a diagnostic tool has yet to be widely established, which is crucial for successfully implementing the technique. A clear definition of diagnostic algorithms that include mNGS is vital to show clinical utility. Similarly to real-time PCR, mNGS will one day become a vital tool in any testing algorithm.
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Affiliation(s)
- Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Hayley Cassidy
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Nilay Peker
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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24
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Liu WD, Yen TY, Liu PY, Wu UI, Bhan P, Li YC, Chi CH, Sheng WH. Clinical Application of Metagenomic Next-Generation Sequencing in Patients with Hematologic Malignancies Suffering from Sepsis. Microorganisms 2021; 9:microorganisms9112309. [PMID: 34835435 PMCID: PMC8624204 DOI: 10.3390/microorganisms9112309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 11/21/2022] Open
Abstract
Background: Sepsis remains a common but fatal complication among patients with immune suppression. We aimed to investigate the performance of metagenomic next-generation sequencing (mNGS) compared with standard microbiological diagnostics in patients with hematologic malignancies. Methods: We performed a prospective study from June 2019 to December 2019. Adult patients with hematologic malignancies and a clinical diagnosis of sepsis were enrolled. Conventional diagnostic methods included blood cultures, serum galactomannan for Aspergillus, cryptococcal antigen and cytomegalovirus (CMV) viral loads. Blood samples for mNGS were collected within 24 h after hypotension developed. Results: Of 24 patients enrolled, mNGS and conventional diagnostic methods (blood cultures, serology testing and virus RT-PCR) reached comparable positive results in 9 cases. Of ten patients, mNGS was able to identify additional pathogens compared with conventional methods; most of the pathogens were virus. Conclusion: Our results show that mNGS may serve as adjunctive diagnostic tool for the identification of pathogens of hematologic patients with clinically sepsis.
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Affiliation(s)
- Wang-Da Liu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 100, Taiwan; (W.-D.L.); (P.-Y.L.); (U.-I.W.)
- Department of Medicine, National Taiwan University Cancer Center, Taipei 106, Taiwan
| | - Ting-Yu Yen
- Department of Pediatrics, National Taiwan University Children’s Hospital, Taipei 100, Taiwan;
| | - Po-Yo Liu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 100, Taiwan; (W.-D.L.); (P.-Y.L.); (U.-I.W.)
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London AL9 7TA, UK
| | - Un-In Wu
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 100, Taiwan; (W.-D.L.); (P.-Y.L.); (U.-I.W.)
- Department of Medicine, National Taiwan University Cancer Center, Taipei 106, Taiwan
| | - Prerana Bhan
- LIHPAO Life Science Cooperation, New Taipei City 251, Taiwan; (P.B.); (Y.-C.L.); (C.-H.C.)
| | - Yu-Chi Li
- LIHPAO Life Science Cooperation, New Taipei City 251, Taiwan; (P.B.); (Y.-C.L.); (C.-H.C.)
| | - Chih-Hung Chi
- LIHPAO Life Science Cooperation, New Taipei City 251, Taiwan; (P.B.); (Y.-C.L.); (C.-H.C.)
| | - Wang-Huei Sheng
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 100, Taiwan; (W.-D.L.); (P.-Y.L.); (U.-I.W.)
- Department of Medical Education, National Taiwan University Hospital, Taipei 100, Taiwan
- School of Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan
- Correspondence:
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25
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Rello J, Alonso-Tarrés C. Emerging Technologies for Microbiologic Diagnosis of Sepsis: The rapid determination of resistance to antimicrobial agents should be the key. Clin Infect Dis 2021; 73:1173-1175. [PMID: 33895796 DOI: 10.1093/cid/ciab355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jordi Rello
- Clinical Research in Pneumonia & Sepsis (CRIPS). Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.,Clinical Research. CHU Maribeau. Nîmes, France
| | - Carles Alonso-Tarrés
- Microbiology Department, Laboratory. Fundació Puigvert. Barcelona, Spain.,Universitat Autònoma de Barcelona, Spain
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