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Cao H, Chen Y, Ge L, Kwong JSW, Lai H, Hu F, Zhang R, Zhao H, Hu L, He R, Zheng W, Zhang J. An umbrella review of the diagnostic value of next-generation sequencing in infectious diseases. Int J Clin Pharm 2024; 46:780-794. [PMID: 38570474 DOI: 10.1007/s11096-024-01704-2] [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: 12/15/2023] [Accepted: 01/18/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND An increasing number of systematic reviews (SRs) have evaluated the diagnostic values of next-generation sequencing (NGS) in infectious diseases (IDs). AIM This umbrella analysis aimed to assess the potential risk of bias in existing SRs and to summarize the published diagnostic values of NGS in different IDs. METHOD We searched PubMed, Embase, and the Cochrane Library until September 2023 for SRs assessing the diagnostic validity of NGS for IDs. Two investigators independently determined review eligibility, extracted data, and evaluated reporting quality, risk of bias, methodological quality, and evidence certainty in the included SRs. RESULTS Eleven SRs were analyzed. Most SRs exhibited a moderate level of reporting quality, while a serious risk of bias was observed in all SRs. The diagnostic performance of NGS in detecting pneumocystis pneumonia and periprosthetic/prosthetic joint infection was notably robust, showing excellent sensitivity (pneumocystis pneumonia: 0.96, 95% CI 0.90-0.99, very low certainty; periprosthetic/prosthetic joint infection: 0.93, 95% CI 0.83-0.97, very low certainty) and specificity (pneumocystis pneumonia: 0.96, 95% CI 0.92-0.98, very low certainty; periprosthetic/prosthetic joint infection: 0.95, 95% CI 0.92-0.97, very low certainty). NGS exhibited high specificity for central nervous system infection, bacterial meningoencephalitis, and tuberculous meningitis. The sensitivity to these infectious diseases was moderate. NGS demonstrated moderate sensitivity and specificity for multiple infections and pulmonary infections. CONCLUSION This umbrella analysis indicates that NGS is a promising technique for diagnosing pneumocystis pneumonia and periprosthetic/prosthetic joint infection with excellent sensitivity and specificity. More high-quality original research and SRs are needed to verify the current findings.
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Affiliation(s)
- Hong Cao
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Yan Chen
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Long Ge
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Joey Sum-Wing Kwong
- Global Health Nursing, Graduate School of Nursing Science, St. Luke's International University, 10-1 Akashi-Cho, Chuo-Ku, Tokyo, 104-0044, Japan
| | - Honghao Lai
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Fangfang Hu
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, 550002, Guizhou Province, China
| | - Rui Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Huaye Zhao
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Linfang Hu
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Rui He
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Wenyi Zheng
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Jiaxing Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China.
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Gaillard T, Dupieux-Chabert C, Roux AL, Tessier E, Boutet-Dubois A, Courboulès C, Corvec S, Bémer P, Lavigne JP, El Sayed F, Marchandin H, Munier C, Chanard E, Gazzano V, Loiez C, Laurent F. A prospective multicentre evaluation of BioFire® Joint Infection Panel for the rapid microbiological documentation of acute arthritis. Clin Microbiol Infect 2024; 30:905-910. [PMID: 38522842 DOI: 10.1016/j.cmi.2024.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
OBJECTIVES To assess the performance of the rapid syndromic BioFire® Joint Infection Panel (BF-JIP) to detect bacterial and fungal pathogens, as well as antibiotic resistance genes, directly in synovial fluid specimens collected from patients with acute arthritis. METHODS The study was conducted in six French bacteriological laboratories. To assess the performances of BF-JIP, results were compared with those of synovial fluid 14-day culture and, in case of discrepancy, with those of complementary molecular methods and intraoperative samples. A total of 308 synovial fluid specimens were tested after collection from 308 adults and children presenting with clinical and biological suspicion of acute arthritis; patients presenting with acute periprosthetic joint infection were included according to the European Bone and Joint Infection Society 2021 criteria. RESULTS Only one specimen failed (no result). On the basis of the consolidated data, the BF-JIP was concordant with the 14-day culture in 280 (91.2%) of the 307 specimens finally included in the study. The positive percentage agreement was 84.9% (95% CI, 78.8-89.8%) and the negative percentage agreement was 100% (95% CI, 97.2-100%). The positive predictive value was extremely high (100%; 95% CI, 97.6-100%), whereas the negative predictive value was lower (82.6%; 95% CI, 75.7-88.2%), partially explained by the missing target species in the panel. DISCUSSION The BF-JIP showed high performances to detect pathogens involved in acute arthritis.
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Affiliation(s)
- Tiphaine Gaillard
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Hôpital Croix-Rousse, Lyon, France.
| | - Céline Dupieux-Chabert
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Hôpital Croix-Rousse, Lyon, France
| | - Anne-Laure Roux
- Département de Microbiologie, Ambroise Paré University Hospital, Boulogne-Billancourt, France
| | - Eve Tessier
- Département de Bactériologie, Centre Hospitalo-Universitaire de Nantes, Nantes, France
| | - Adeline Boutet-Dubois
- Département de Microbiologie et d'hygiène Hospitalière, Centre Hospitalo-Universitaire de Nîmes, Nîmes, France
| | - Camille Courboulès
- Département de Microbiologie, Ambroise Paré University Hospital, Boulogne-Billancourt, France
| | - Stéphane Corvec
- Département de Bactériologie, Centre Hospitalo-Universitaire de Nantes, Nantes, France
| | - Pascale Bémer
- Département de Bactériologie, Centre Hospitalo-Universitaire de Nantes, Nantes, France
| | - Jean-Philippe Lavigne
- Département de Microbiologie et d'hygiène Hospitalière, Centre Hospitalo-Universitaire de Nîmes, Nîmes, France
| | - Faten El Sayed
- Département de Microbiologie, Ambroise Paré University Hospital, Boulogne-Billancourt, France
| | - Hélène Marchandin
- Département de Microbiologie et d'hygiène Hospitalière, Centre Hospitalo-Universitaire de Nîmes, Nîmes, France
| | - Clément Munier
- Département de Microbiologie, Cerballiance Rhône-Alpes, Lyon, France
| | - Emmanuel Chanard
- Département de Microbiologie, Cerballiance Rhône-Alpes, Lyon, France
| | - Vincent Gazzano
- Département de Microbiologie, Cerballiance Rhône-Alpes, Lyon, France
| | - Caroline Loiez
- Centre Hospitalo-Universitaire de Lille, Institut de Microbiologie - Centre de Biologie Pathologie, Service Bactériologie, Lille, France
| | - Frédéric Laurent
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Hôpital Croix-Rousse, Lyon, France
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Zhou H, Yang Y, Zhang Y, Li F, Shen Y, Qin L, Huang W. Current Status and Perspectives of Diagnosis and Treatment of Periprosthetic Joint Infection. Infect Drug Resist 2024; 17:2417-2429. [PMID: 38912221 PMCID: PMC11192293 DOI: 10.2147/idr.s457644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
Periprosthetic joint infection (PJI) is a catastrophic complication following joint replacement surgery, posing significant challenges to orthopedic surgeons. Due to the lack of a definitive diagnostic gold standard, timely treatment initiation is problematic, resulting in substantial economic burdens on patients and society. In this review, we thoroughly analyze the complexities of PJI and emphasize the importance of accurate diagnosis and effective treatment. The article specifically focuses on the advancements in diagnostic techniques, ranging from traditional pathogen culture to advanced molecular diagnostics, and discusses their role in enhancing diagnostic accuracy. Additionally, we review the latest surgical management strategies, including everything from debridement to revision surgeries. Our summary aims to provide practical information for the diagnosis and treatment of PJI and encourages further research to improve diagnostic accuracy and treatment outcomes.
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Affiliation(s)
- Haotian Zhou
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yaji Yang
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yanhao Zhang
- College of Pharmacy, Army Military Medical University, Chongqing, 400038, People’s Republic of China
| | - Feilong Li
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Yidong Shen
- Department of Orthopaedics, The First People’s Hospital of Yancheng, Yancheng, 224000, People’s Republic of China
| | - Leilei Qin
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Wei Huang
- Department of Orthopaedics, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, People’s Republic of China
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Ye J, Huang K, Xu Y, Chen N, Tu Y, Huang J, Shao L, Kong W, Zhao D, Xie Y. Clinical application of nanopore-targeted sequencing technology in bronchoalveolar lavage fluid from patients with pulmonary infections. Microbiol Spectr 2024; 12:e0002624. [PMID: 38687074 DOI: 10.1128/spectrum.00026-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
The rapid and effective identification of pathogens in patients with pulmonary infections has posed a persistent challenge in medicine, with conventional microbiological tests (CMTs) proving time-consuming and less sensitive, hindering early diagnosis of respiratory infections. While there has been some research on the clinical performance of targeted sequencing technologies, limited focus has been directed toward bronchoalveolar lavage fluid (BALF). This study primarily evaluates the pathogen detection capabilities of nanopore-targeted sequencing (NTS) in BALF, providing a comprehensive analysis. The retrospective study, spanning from January 2022 to November 2023, includes 223 patients exclusively sourced from a single center. We conducted a detailed comparative analysis among NTS, targeted next-generation sequencing (tNGS), and CMTs. Initially, we compared the detection capabilities of NTS and tNGS and found no significant differences in their sensitivity and specificity. Specifically, we observed that the sensitivity of NTS was significantly higher than that of CMTs (74.83% vs 33.11%, P < 0.001). Furthermore, NTS exhibited a higher positivity rate in common pulmonary infections (62.88% vs. 23.48%) and in clinically suspected tuberculosis patients compared to CMTs (87.18% vs. 48.72%). Additionally, NTS showed less susceptibility to antibiotic interference, indicating a more sensitive detection capability, especially in detecting fastidious organisms. It complements GeneXpert in tuberculosis diagnosis and offers excellent advantages in identifying pathogens challenging for CMTs, such as non-tuberculous mycobacteria and viruses. Moreover, NTS significantly shortens the reporting time and is only a quarter of the cost of metagenomic next-generation sequencing. Clearly, NTS can facilitate faster and more cost-effective early diagnosis of respiratory infections.IMPORTANCEThis study holds paramount significance in advancing the field of respiratory infection diagnostics. By assessing the pathogen detection capabilities in bronchoalveolar lavage fluid (BALF) of patients with pulmonary infections, we illuminate the promising potential of nanopore-targeted sequencing (NTS). The findings underscore NTS as a comparable yet distinct alternative to traditional methods like comprehensive conventional microbiological tests (CMTs). Notably, NTS demonstrates a pivotal edge, expanding the spectrum of identified pathogens, particularly excelling in the detection of challenging entities like non-tuberculous mycobacteria and viruses. The study also highlights the complementary role of NTS alongside GeneXpert in the identification of tuberculosis, providing a comprehensive overview of the diagnostic landscape for respiratory infections. This insight carries significant implications for clinicians seeking rapid, cost-effective, and accurate diagnostic tools in the realm of pulmonary infections.
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Affiliation(s)
- Jiayuan Ye
- Health Science Center, Ningbo University, Ningbo, Zhejiang, China
- Department of Infectious Diseases, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Kai Huang
- Department of General Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Yaojiang Xu
- Department of Infectious Diseases, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Nan Chen
- Department of Infectious Diseases, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Yifei Tu
- Department of Radiology, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Jing Huang
- Department of Respiratory, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Longfei Shao
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Weiliang Kong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yilian Xie
- Department of Infectious Diseases, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
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Wang Q, Chen Y, Chen Y, Lv J, Ding H, Huang J, Huang J, Huang Z, Yang B, Zhang W, Fang X. Improved cure rate of periprosthetic joint infection through targeted antibiotic therapy based on integrated pathogen diagnosis strategy. Front Cell Infect Microbiol 2024; 14:1388385. [PMID: 38836059 PMCID: PMC11148460 DOI: 10.3389/fcimb.2024.1388385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/18/2024] [Indexed: 06/06/2024] Open
Abstract
Objectives This study aimed to determine whether combined of pathogen detection strategies, including specimen acquisition, culture conditions, and molecular diagnostics, can improve treatment outcomes in patients with periprosthetic joint infections (PJI). Methods This retrospective study included suspected PJI cases from three sequential stages at our institution: Stage A (July 2012 to June 2015), Stage B (July 2015 to June 2018), and Stage C (July 2018 to June 2021). Cases were categorized into PJI and aseptic failure (AF) groups based on European Bone and Joint Infection Society (EBJIS) criteria. Utilization of pathogen diagnostic strategies, pathogen detection rates, targeted antibiotic prescription rates, and treatment outcomes were analyzed and compared across the three stages. Results A total of 165 PJI cases and 38 AF cases were included in this study. With the progressive implementation of the three optimization approaches across stages A, B and C, pathogen detection rates exhibited a gradual increase (χ2 = 8.282, P=0.016). Similarly, utilization of targeted antibiotic therapy increased stepwise from 57.1% in Stage A, to 82.3% in Stage B, and to 84% in Stage C (χ2 = 9.515, P=0.009). The 2-year infection control rate exceeded 90% in both stages B and C, surpassing stage A (71.4%) (χ2 = 8.317, P=0.011). Combined application of all three optimized protocols yielded the highest sensitivity of 91.21% for pathogen detection, while retaining higher specificity of 92.11%. Conclusion The utilization of combined pathogen diagnostic strategies in PJI can increase pathogen detection rates, improve targeted antibiotic prescription, reduce the occurrence of antibiotic complications, and achieve better treatment outcomes.
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Affiliation(s)
- Qijin Wang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, The Affiliated Mindong Hospital of Fujian Medical University, Fuan, China
| | - Yongfa Chen
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yang Chen
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jianhua Lv
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Haiqi Ding
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jiagu Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jiexin Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, 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, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, 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, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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Wang B, Wang Q, Li M, Yu J, Jiang F, Hu Y, Guo G, Chen X, Tang J, Han P, Shen H. Diagnostic Role of Metagenomic Next-Generation Sequencing in Tubercular Orthopedic Implant-Associated Infection. Infect Drug Resist 2024; 17:1951-1960. [PMID: 38774035 PMCID: PMC11107837 DOI: 10.2147/idr.s441940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
Objective The diagnosis of tubercular orthopedic implant-associated infection (TB-IAI) is challenging. This study evaluated the value of metagenomic next-generation sequencing (mNGS) for the diagnosis of TB-IAI and developed a standardized diagnostic procedure for TB-IAI. Methods The records of all patients with TB-IAI diagnosed and treated at our institution between December 2018 and September 2022 were retrospectively reviewed. Patient demographic characteristics, medical history, laboratory test, microbial culture, histopathology, and mNGS results, and time to diagnosis were recorded. The diagnostic efficiency of mNGS for TB-IAI was assessed by comparing the results and diagnostic time with that of other diagnostic modalities. Results Ten patients were included in the analysis, including eight with prosthetic joint infections and two with fracture-related infections. The mNGS positivity rate was 100% (10/10), which was higher than that of TB-antibody (11%, 1/9), real-time quantitative polymerase chain reaction (22%, 2/9), T-SPOT.TB (25%, 2/8), purified protein derivative (50%, 4/8), microbial culture (50%, 5/10), and histopathology (20%, 2/10). mNGS shortened the time to diagnosis of TB-IAI. A standardized diagnostic procedure for TB-IAI was developed based on the findings. Conclusion mNGS is useful for the diagnosis of TB-IAI. mNGS is recommended in cases where it is difficult to identify a pathogen using routine diagnostic tests. The standardized diagnostic procedure might improve TB-IAI diagnosis. Importance TB-IAI is a rare infection, which occurs after orthopedic surgery and hard to diagnose microbiologically. mNGS is a new detection technique not yet discussed in current literature as a means for TB-IAI diagnostics. Here we describe a cohort of patients with TB-IAI diagnosed by mNGS show high efficiency of mNGS for detection of this pathology and present a clinical algorithm supplementing conventional methods for TB-IAI assessment.
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Affiliation(s)
- Boyong Wang
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Qiaojie Wang
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Mingzhang Li
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Jinlong Yu
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Feng Jiang
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Yujie Hu
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Geyong Guo
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Xiaohua Chen
- Department of Infectious Diseases, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Jin Tang
- Clinical Laboratory, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Pei Han
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
| | - Hao Shen
- Department of Orthopedics, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, People’s Republic of China
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Su S, Wang R, Zhou R, Bai J, Chen Z, Zhou F. Higher diagnostic value of next-generation sequencing versus culture in periprosthetic joint infection: A systematic review and meta-analysis. Knee Surg Sports Traumatol Arthrosc 2024. [PMID: 38713871 DOI: 10.1002/ksa.12227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND The next-generation sequencing (NGS) has developed rapidly in the past decade and is becoming a promising diagnostic tool for periprosthetic infection (PJI). However, its diagnostic value for PJI is still uncertain. The purpose of this systematic review and meta-analysis was to evaluate the diagnostic value of NGS compared to culture. METHODS In this systematic review and meta-analysis, electronic databases including PubMed, Embase, Cochrane Central Register of Controlled Trials, Web of Science and clinicaltrials.gov were searched for studies from inception to 12 November 2023. Diagnostic parameters, such as sensitivity, specificity, diagnostic odds ratio and area under the summary receiver-operating characteristic (SROC) curve (AUC), were calculated for the included studies. A systematic review and meta-analysis was performed. RESULTS A total of 22 studies with 2461 patients were included in our study. The pooled sensitivity, specificity and diagnostic odds ratio of NGS were 87% (95% confidence interval [CI]: 83-90), 94% (95% CI: 91-96) and 111 (95% CI: 70-177), respectively. On the other hand, the pooled sensitivity, specificity and diagnostic odds ratio of culture were 63% (95% CI: 58-67), 98% (95% CI: 96-99) and 93 (95% CI: 40-212), respectively. The SROC curve for NGS and culture showed that the AUCs are 0.96 (95% CI: 0.94-0.98) and 0.82 (95% CI: 0.79-0.86), respectively. CONCLUSION This systematic review and meta-analysis found NGS had higher sensitivity and diagnostic accuracy but slightly lower specificity than culture. Based on the pooled results, we suggested NGS may have the potential to be a new tool for the diagnosis of PJI. LEVEL OF EVIDENCE Level IV.
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Affiliation(s)
- Shilong Su
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Ruideng Wang
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Rubing Zhou
- Department of Orthopedics, Beijing friendship hospital, Capital Medical University, Xicheng, Beijing, China
| | - Jinwu Bai
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Zhengyang Chen
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Fang Zhou
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
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8
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Mahnic A, Rak M, Trebše R, Rupnik M, Cőr A. Identification of prosthetic joint infections with 16S amplicon metagenomic sequencing - comparison with standard cultivation approach. Diagn Microbiol Infect Dis 2024; 109:116188. [PMID: 38340614 DOI: 10.1016/j.diagmicrobio.2024.116188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024]
Abstract
Prosthetic joint infections (PJIs) are commonly diagnosed via culture-based methods, which may miss hard-to-grow pathogens. This study contrasts amplicon metagenomic sequencing (16S AS) with traditional culture techniques for enhanced clinical decision-making. We analyzed sonicate fluid from 27 patients undergoing revision arthroplasty using both methods, emphasizing the distinction between contaminants and true positives. Our findings show moderate agreement between the two methods, with a Cohen's kappa of 0.490, varying across bacterial genera (Cohen's kappa -0.059 to 1). The sensitivity of 16S AS compared to culture was 81% (95% CI, 68% to 94%). Sequencing revealed greater microbial diversity, including anaerobic genera like Anaerococcus and Citrobacter. Interestingly, several culture-negative PJI samples showed diverse bacteria via 16S AS. Despite rigorous controls and algorithms to eliminate contaminants, confirming bacteria presence with 16S AS remains a challenge. This highlights the need for improved PJI diagnostic methods, while also pointing out the limitations of next-generation sequencing (NGS) as a clinical diagnostic tool.
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Affiliation(s)
- Aleksander Mahnic
- National Laboratory of Health, Environment and Food, Department for Microbiological Research, Maribor, Slovenia.
| | - Mitja Rak
- National Laboratory of Health, Environment and Food, Medical Microbiology Department, Koper, Slovenia
| | - Rihard Trebše
- Orthopaedic Hospital Valdoltra, Ankaran, Slovenia; Faculty of Medicine, University of Ljubljana, Slovenia
| | - Maja Rupnik
- National Laboratory of Health, Environment and Food, Department for Microbiological Research, Maribor, Slovenia; Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Andrej Cőr
- Orthopaedic Hospital Valdoltra, Ankaran, Slovenia; University of Primorska, Faculty of Health Sciences, Izola, Slovenia
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9
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Zheng YR, Chen XH, Chen Q, Cao H. Metagenomic Next-generation Sequencing for Pathogen Identification in Bronchoalveolar Lavage Fluid From Neonates Receiving Extracorporeal Membrane Oxygenation. Pediatr Infect Dis J 2024; 43:371-377. [PMID: 38306604 DOI: 10.1097/inf.0000000000004250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
BACKGROUND Neonates on extracorporeal membrane oxygenation (ECMO) are at high risk of infection. Rapid and accurate identification of pathogens is essential to improve the prognosis of children on ECMO. Metagenome next-generation sequencing (mNGS) has been used in recent years to detect pathogenic bacteria, but evidence for its use in neonates on ECMO is lacking. METHODS This retrospective study was conducted using an electronic medical record system. We analyzed the results of mNGS and conventional microbiological tests (CMTs) in bronchoalveolar lavage fluid of neonates receiving ECMO support with pulmonary infections in our hospital from July 2021 to January 2023. RESULTS We screened 18 ECMO-supported neonates with pneumonia for inclusion in the study. The median age of the included children was 2 (1-4) days, the median gestational age was 38.3 (33-40 +4 ) weeks, and the median weight was 3.3 (2.2-4.8) kg. The detection rate of mNGS was 77.8% (14/18), higher than the 44.4% (8/18) of CMT ( P = 0.04). A total of 20 pathogens were detected in mNGS, with the top 3 most common pathogens being Klebsiella pneumoniae , Acinetobacter baumannii and Escherichia coli . Mixed infections were found in 14 cases (77.8%), including 13 cases (72.2%) with mixed infections detected by mNGS and 7 cases (27.8%) with mixed infections detected by CMT. A total of 9 children underwent treatment changes based on mNGS results and all of them experienced relief of symptoms. CONCLUSION Compared with CMT, mNGS can detect pathogens earlier and more sensitively, and may play an important role in ECMO-supported neonatal pneumonia pathogen detection and optimization of antibiotic therapy.
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Affiliation(s)
- Yi-Rong Zheng
- From the Department of Cardiac Surgery, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), Fuzhou, China
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10
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Ramachandran PS, Williamson DA. The transformative potential of metagenomics in microbiology: advancements and implications. Intern Med J 2023; 53:1520-1523. [PMID: 37743240 DOI: 10.1111/imj.16228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/20/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Prashanth S Ramachandran
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Melbourne, Australia
- Department of Neurology, Royal Melbourne Hospital, Victoria, Melbourne, Australia
- Department of Neurology, St. Vincent's Hospital, Victoria, Melbourne, Australia
| | - Deborah A Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Melbourne, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Victoria, Melbourne, Australia
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11
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Hantouly AT, Alzobi O, Toubasi AA, Zikria B, Al Dosari MAA, Ahmed G. Higher sensitivity and accuracy of synovial next-generation sequencing in comparison to culture in diagnosing periprosthetic joint infection: a systematic review and meta-analysis. Knee Surg Sports Traumatol Arthrosc 2023; 31:3672-3683. [PMID: 36244018 PMCID: PMC10435641 DOI: 10.1007/s00167-022-07196-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/02/2022] [Indexed: 12/29/2022]
Abstract
PURPOSE The purpose of this meta-analysis was to compare the diagnostic parameters of synovial next-generation sequencing (NGS) and cultures in diagnosing periprosthetic joint infections (PJI). METHODS PubMed, Web of Science, Cochrane, and Google Scholar were searched from inception until 8 Jan 2022 for literature investigating the role of NGS in comparison to culture in the diagnosis of PJI. The studies were included if they investigated the diagnostic value of culture and NGS in diagnosing PJIs against the Musculoskeletal Infection Society (MSIS) criteria. Diagnostic parameters, such as sensitivity, specificity, positive predictive value, negative predictive value, positive-likelihood ratio, negative-likelihood ratio, accuracy, and area under the curve (AUC), were calculated for the included studies to evaluate the performance of NGS in comparison to culture in PJI diagnosis. RESULTS The total number of the included patients was 341 from seven articles. The pooled sensitivity, specificity, and diagnostic odds ratio of NGS were 94% (95% CI 91-97%), 89% (95% CI 82-95%), and 138.5 (95% CI 49.1-390.5), respectively. NGS has positive- and negative-likelihood ratios of 7.9 (95% CI 3.99-15.6) and 0.1 (95% CI 0.0-0.1), respectively. On the other hand, the pooled sensitivity, specificity, and diagnostic odds ratio of culture were 70% (95% CI 61-79%), 94% (95% CI 88-98%), and 28.0 (95% CI 12.6-62.2), respectively. The SROC curve for NGS showed that the accuracy (AUC) was 91.9%, and that the positive and negative predictive values were 8.6 (95% CI 5.0-19.5) and 0.1 (95% CI 0.0-0.1), respectively. While, culture SROC curve demonstrated that the accuracy (AUC) was 80.5% and the positive- and negative-likelihood ratio were 12.1 (95% CI 4.5-49.6) and 0.3 (95% CI 0.2-0.4). CONCLUSIONS NGS has a potential role in diagnosing hip and knee PJIs due to its high sensitivity, specificity, and accuracy. However, the sensitivity and specificity reported by the studies varied according to the time of synovial sampling (preoperative, postoperative, or mixed).
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Affiliation(s)
- Ashraf T Hantouly
- Department of Orthopedic Surgery, Surgical Specialty Center, Hamad Medical Corporation, Doha, Qatar
| | - Osama Alzobi
- Department of Orthopedic Surgery, Surgical Specialty Center, Hamad Medical Corporation, Doha, Qatar
| | | | - Bashir Zikria
- Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| | | | - Ghalib Ahmed
- Department of Orthopedic Surgery, Surgical Specialty Center, Hamad Medical Corporation, Doha, Qatar.
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12
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Ponraj DS, Lund M, Lange J, Poehlein A, Himmelbach A, Falstie-Jensen T, Jørgensen NP, Ravn C, Brüggemann H. Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent. Front Cell Infect Microbiol 2023; 13:1165017. [PMID: 37265503 PMCID: PMC10229904 DOI: 10.3389/fcimb.2023.1165017] [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: 02/13/2023] [Accepted: 05/02/2023] [Indexed: 06/03/2023] Open
Abstract
Orthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed on sonication fluid (SF) specimens derived from 24 implants. These were divided into three groups, based on culture results: group I, culture-negative (n = 4); group II, culture-positive for C. acnes (n = 10); and group III, culture-positive for other bacteria (n = 10). In group I, sequence reads from C. acnes were detected in only one SF sample, originating from a suspected case of OIAIs, which was SF and tissue culture-negative. In group II, C. acnes sequences were detected in 7/10 samples. In group III, C. acnes sequence reads were found in 5/10 samples, in addition to sequence reads that matched the bacterial species identified by culture. These samples could represent polymicrobial infections that were missed by culture. Taken together, mNGS was able to detect C. acnes DNA in more samples compared to culture and could be used to identify cases of suspected C. acnes OIAIs, in particular regarding possible polymicrobial infections, where the growth of C. acnes might be compromised due to a fast-growing bacterial species. However, since SF specimens are usually low-biomass samples, mNGS is prone to DNA contamination, possibly introduced during DNA extraction or sequencing procedures. Thus, it is advisable to set a sequence read count threshold, taking into account project- and NGS-specific criteria.
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Affiliation(s)
| | - Michael Lund
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jeppe Lange
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Orthopaedic Surgery, Regional Hospital, Horsens, Denmark
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | | | - Christen Ravn
- Department of Orthopaedic Surgery, Aarhus University Hospital, Aarhus, Denmark
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13
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Hao L, Wen P, Song W, Zhang B, Wu Y, Zhang Y, Ma T, Qiu Y. Direct detection and identification of periprosthetic joint infection pathogens by metagenomic next-generation sequencing. Sci Rep 2023; 13:7897. [PMID: 37193765 DOI: 10.1038/s41598-023-35215-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/15/2023] [Indexed: 05/18/2023] Open
Abstract
This study assessed the application of metagenomic next-generation sequencing in pathogen detection of periprosthetic joint infections. A total of 95 cases who previously had undergone hip and knee replacement undergoing revision from January 2018 to January 2021 were included in this study. Specimens of synovial fluid and deep-tissue were collected for culture and metagenomic next-generation sequencing, and patients were retrospectively categorized as infected or aseptic using the Musculoskeletal Infection Society criteria after revision surgery. The sensitivity, specificity, positive and negative predictive values were compared. A total of 36 cases had positive culture results and 59 cases had positive metagenomic next-generation sequencing results. Culture was positive in 34 infected cases (58.6%) and 2 aseptic cases (5.4%). Metagenomic next-generation sequencing was positive in 55 infected cases (94.8%) and 4 aseptic cases (10.8%). Five cases diagnosed with infection had other potential pathogens detected by metagenomic next-generation sequencing. Among the 24 culture-negative periprosthetic joint infections, metagenomic next-generation sequencing was able to identify potential pathogens in 21 cases (87.5%). From sampling to reporting, the average time needed for culture was 5.2 (95% CI 3.1-7.3) days, while that for metagenomic next-generation sequencing was 1.3 (95% CI 0.9-1.7) days. Metagenomic next-generation sequencing is more advantageous in pathogen detection of periprosthetic joint infection after total joint replacement, especially in patients with multiple infections or negative culture results.
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Affiliation(s)
- Linjie Hao
- Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China
| | - Pengfei Wen
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China
| | - Wei Song
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China
| | - Binfei Zhang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China
| | - Yanjie Wu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China
| | - Yumin Zhang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China.
| | - Tao Ma
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, 555 East Youyi Road, Xi'an, 710000, Shaanxi, China.
| | - Yusheng Qiu
- Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
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14
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Cretu B, Iordache S, Cursaru A, Serban B, Costache M, Cirstoiu C, Spiridonica R. Metagenomic Next-Generation Sequencing for Periprosthetic Joint Infections. Cureus 2023; 15:e38726. [PMID: 37168414 PMCID: PMC10166283 DOI: 10.7759/cureus.38726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
Periprosthetic joint infection (PJI) after arthroplasty is a major complication, which requires significant resources, resulting in high costs for the medical system. In recent years, significant progress has been made in the diagnosis and treatment of periprosthetic infections, the identification of the pathogen being the central element in the establishment of targeted antibiotic therapy. Next-generation sequencing (NGS) or metagenomic NGS (mNGS) represents a promising, fast alternative, with increased specificity and sensitivity compared to identification methods using conventional culture media, thus enabling an increased rate of identification of pathogenic microorganisms and antibiotic resistance genes (ARG). The purpose of this article was to highlight new molecular diagnostic methods for periprosthetic joint infections and their involvement in treatment efficiency. NGS technologies are cutting-edge techniques that may challenge the PJI diagnostic model.
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Affiliation(s)
- Bogdan Cretu
- Orthopedics and Traumatology, University Emergency Hospital, Bucharest, ROU
| | - Sergiu Iordache
- Orthopedics and Traumatology, University Emergency Hospital, Bucharest, ROU
| | - Adrian Cursaru
- Orthopedics and Traumatology, University Emergency Hospital, Bucharest, ROU
| | - Bogdan Serban
- Orthopedics and Traumatology, University Emergency Hospital, Bucharest, ROU
| | - Mihai Costache
- Orthopedics and Traumatology, University Emergency Hospital, Bucharest, ROU
| | - Catalin Cirstoiu
- Orthopedics and Traumatology, University Emergency Hospital, Bucharest, ROU
| | - Razvan Spiridonica
- Orthopedics and Traumatology, University Emergency Hospital, Bucharest, ROU
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15
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Serbanescu MA, Apple CG, Fernandez-Moure JS. Role of Resident Microbial Communities in Biofilm-Related Implant Infections: Recent Insights and Implications. Surg Infect (Larchmt) 2023; 24:258-264. [PMID: 37010966 PMCID: PMC11074437 DOI: 10.1089/sur.2023.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
The use of medical implants continues to grow as the population ages. Biofilm-related implant infection is the leading cause of medical implant failure and remains difficult to diagnose and treat. Recent technologies have enhanced our understanding of the composition and complex functions of microbiota occupying various body site niches. In this review, we leverage data from molecular sequencing technologies to explore how silent changes in microbial communities from various sites can influence the development of biofilm-related infections. Specifically, we address biofilm formation and recent insights of the organisms involved in biofilm-related implant infections; how composition of microbiomes from skin, nasopharyngeal, and nearby tissue can impact biofilm-formation, and infection; the role of the gut microbiome in implant-related biofilm formation; and therapeutic strategies to mitigate implant colonization.
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Affiliation(s)
- Mara A. Serbanescu
- Department of Anesthesia, Acute Care Surgery, and Surgical Critical Care, Department of Surgery, Duke University Medical Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Camille G. Apple
- Division of Trauma, Acute Care Surgery, and Surgical Critical Care, Department of Surgery, Duke University Medical Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joseph S. Fernandez-Moure
- Division of Trauma, Acute Care Surgery, and Surgical Critical Care, Department of Surgery, Duke University Medical Center, Duke University School of Medicine, Durham, North Carolina, USA
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Zhang B, Li M, Liu Y, Zhang B, Liu Z, Chen X, Huo J, Han Y. The diagnostic value of blood sample NGS in patients with early periprosthetic joint infection after total hip arthroplasty. Int Wound J 2023; 20:961-970. [PMID: 36054590 PMCID: PMC10030938 DOI: 10.1111/iwj.13943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022] Open
Abstract
The diagnostic value of next-generation sequencing (NGS) of blood samples from patients with periprosthetic joint infection (PJI) after total hip arthroplasty (THA) was evaluated by comparing it with drainage fluid NGS and bacterial culture. The study was designed as a retrospective diagnostic test. Thirty-six infected patients were diagnosed with PJI according to the Musculoskeletal Infection Society (MSIS) criteria and 57 volunteers were included in our study. NGS and bacterial culture were chosen to detect PJI after THA. Blood samples and drainage fluid were collected for NGS, and the drainage fluid, which was collected at the same time as the NGS drainage fluid sample, was used for bacterial culture. The primary outcomes of interest were sensitivity, specificity, and accuracy. In the infection group, 31 patients showed positive results by blood sample NGS, 33 patients showed positive results by drainage fluid NGS, and 17 patients showed positive bacterial culture results. In the control group, the results of 2 blood sample NGS, 16 drainage fluid NGS, and 3 bacterial cultures were positive. The sensitivity, specificity, and accuracy of the blood sample were 0.86, 0.96, and 0.92, respectively. The sensitivity, specificity, and accuracy of the drainage fluid samples were 0.92, 0.72, and 0.80, respectively. The sensitivity, specificity, and accuracy of bacterial culture were 0.47, 0.95, and 0.79, respectively. The study demonstrated that both the sensitivity and specificity of NGS were higher than those of bacterial culture, regardless of the kind of sample. Compared with drainage fluid NGS, the sensitivity of blood sample NGS was slightly lower (0.86 vs 0.92), but blood sample NGS showed higher specificity (0.96 vs 0.72). In total, the diagnostic value of blood sample NGS was superior to that of drainage fluid NGS and bacterial culture. The majority of infected patients could be identified by blood sample NGS. Moreover, because of its high specificity, blood sample NGS can not only detect infectious bacteria but also distinguish infectious from non-infectious bacteria, which is dramatically different from using drainage fluid NGS.
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Affiliation(s)
- Bingshi Zhang
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Mengnan Li
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Yawei Liu
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Binquan Zhang
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Zeming Liu
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Xiao Chen
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Jia Huo
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Yongtai Han
- Department of Osteonecrosis and Hip Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, PR China
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Diagnostic Role of mNGS in Polymicrobial Periprosthetic Joint Infection. J Clin Med 2023; 12:jcm12051838. [PMID: 36902625 PMCID: PMC10003677 DOI: 10.3390/jcm12051838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/02/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
OBJECTIVES The purpose of this study was to explore the clinical value of metagenomic next-generation sequencing (mNGS) in the diagnosis of polymicrobial periprosthetic joint infection (PJI). METHODS Patients with complete data who underwent surgery at our hospital between July 2017 and January 2021 for suspected periprosthetic joint infection (PJI), according to the 2018 ICE diagnostic criteria, were enrolled, and all patients underwent microbial culture and mNGS detection, which were performed on the BGISEQ-500 platform. Microbial cultures were performed on two samples of synovial fluid, six samples of tissue, and two samples of prosthetic sonicate fluid for each patient. The mNGS was performed on 10 tissues, 64 synovial fluid samples, and 17 prosthetic sonicate fluid samples. The results of mNGS testing were based on the interpretation of mNGS results in the previous literature and the assertions of microbiologists and orthopedic surgeons. The diagnostic efficacy of mNGS in polymicrobial PJI was assessed by comparing the results of conventional microbial cultures and mNGS. RESULTS A total of 91 patients were finally enrolled in this study. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of PJI were 71.0%, 95.4%, and 76.9%, respectively. The sensitivity, specificity, and accuracy of mNGS for the diagnosis of PJI were 91.3%, 86.3%, and 90.1%, respectively. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of polymicrobial PJI were 57.1%, 100%, and 91.3%, respectively. mNGS had a sensitivity, specificity, and accuracy of 85.7%, 60.0%, and 65.2%, respectively, for the diagnosis of polymicrobial PJI. CONCLUSIONS mNGS can improve the diagnosis efficiency of polymicrobial PJI, and the combination of culture and mNGS is a promising method to diagnose polymicrobial PJI.
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18
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Advances in the Microbiological Diagnosis of Prosthetic Joint Infections. Diagnostics (Basel) 2023; 13:diagnostics13040809. [PMID: 36832297 PMCID: PMC9954824 DOI: 10.3390/diagnostics13040809] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/31/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
A significant number of prosthetic joint infections (PJI) are culture-negative and/or misinterpreted as aseptic failures in spite of the correct implementation of diagnostic culture techniques, such as tissue sample processing in a bead mill, prolonged incubation time, or sonication of removed implants. Misinterpretation may lead to unnecessary surgery and needless antimicrobial treatment. The diagnostic value of non-culture techniques has been investigated in synovial fluid, periprosthetic tissues, and sonication fluid. Different feasible improvements, such as real-time technology, automated systems and commercial kits are now available to support microbiologists. In this review, we describe non-culture techniques based on nucleic acid amplification and sequencing methods. Polymerase chain reaction (PCR) is a frequently used technique in most microbiology laboratories which allows the detection of a nucleic acid fragment by sequence amplification. Different PCR types can be used to diagnose PJI, each one requiring the selection of appropriate primers. Henceforward, thanks to the reduced cost of sequencing and the availability of next-generation sequencing (NGS), it will be possible to identify the whole pathogen genome sequence and, additionally, to detect all the pathogen sequences present in the joint. Although these new techniques have proved helpful, strict conditions need to be observed in order to detect fastidious microorganisms and rule out contaminants. Specialized microbiologists should assist clinicians in interpreting the result of the analyses at interdisciplinary meetings. New technologies will gradually be made available to improve the etiologic diagnoses of PJI, which will remain an important cornerstone of treatment. Strong collaboration among all specialists involved is essential for the correct diagnosis of PJI.
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Cai Y, Liang J, Chen X, Zhang G, Jing Z, Zhang R, Lv L, Zhang W, Dang X. Synovial fluid neutrophil extracellular traps could improve the diagnosis of periprosthetic joint infection. Bone Joint Res 2023; 12:113-120. [PMID: 36718647 PMCID: PMC9950667 DOI: 10.1302/2046-3758.122.bjr-2022-0391.r1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
AIMS This study aimed to explore the diagnostic value of synovial fluid neutrophil extracellular traps (SF-NETs) in periprosthetic joint infection (PJI) diagnosis, and compare it with that of microbial culture, serum ESR and CRP, synovial white blood cell (WBC) count, and polymorphonuclear neutrophil percentage (PMN%). METHODS In a single health centre, patients with suspected PJI were enrolled from January 2013 to December 2021. The inclusion criteria were: 1) patients who were suspected to have PJI; 2) patients with complete medical records; and 3) patients from whom sufficient synovial fluid was obtained for microbial culture and NET test. Patients who received revision surgeries due to aseptic failure (AF) were selected as controls. Synovial fluid was collected for microbial culture and SF-WBC, SF-PNM%, and SF-NET detection. The receiver operating characteristic curve (ROC) of synovial NET, WBC, PMN%, and area under the curve (AUC) were obtained; the diagnostic efficacies of these diagnostic indexes were calculated and compared. RESULTS The levels of SF-NETs in the PJI group were significantly higher than those of the AF group. The AUC of SF-NET was 0.971 (95% confidence interval (CI) 0.903 to 0.996), the sensitivity was 93.48% (95% CI 82.10% to 98.63%), the specificity was 96.43% (95% CI 81.65% to 99.91%), the accuracy was 94.60% (95% CI 86.73% to 98.50%), the positive predictive value was 97.73%, and the negative predictive value was 90%. Further analysis showed that SF-NET could improve the diagnosis of culture-negative PJI, patients with PJI who received antibiotic treatment preoperatively, and fungal PJI. CONCLUSION SF-NET is a novel and ideal synovial fluid biomarker for PJI diagnosis, which could improve PJI diagnosis greatly.Cite this article: Bone Joint Res 2023;12(2):113-120.
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Affiliation(s)
- Yuanqing Cai
- Department of Orthopaedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China,Department of Orthopaedics, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jialin Liang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Xiaoqing Chen
- Department of Orthopaedics, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Guangyang Zhang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Zhaopu Jing
- Department of Orthopaedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Rupeng Zhang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Leifeng Lv
- Department of Orthopaedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China
| | - Wenming Zhang
- Department of Orthopaedics, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xiaoqian Dang
- Department of Orthopaedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an, China, Xiaoqian Dang. E-mail:
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20
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Affiliation(s)
- Robin Patel
- From the Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, and the Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN
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21
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Han S, Zhao Z, Yang L, Huang J, Wang Y, Feng J. The performance of metagenomic next-generation sequencing in diagnosing pulmonary infectious diseases using authentic clinical specimens: The Illumina platform versus the Beijing Genomics Institute platform. Front Pharmacol 2023; 14:1164633. [PMID: 37138853 PMCID: PMC10149716 DOI: 10.3389/fphar.2023.1164633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction: Metagenomic next-generation sequencing (mNGS) has been increasingly used to detect infectious organisms and is rapidly moving from research to clinical laboratories. Presently, mNGS platforms mainly include those from Illumina and the Beijing Genomics Institute (BGI). Previous studies have reported that various sequencing platforms have similar sensitivity in detecting the reference panel that mimics clinical specimens. However, whether the Illumina and BGI platforms provide the same diagnostic performance using authentic clinical samples remains unclear. Methods: In this prospective study, we compared the performance of the Illumina and BGI platforms in detecting pulmonary pathogens. Forty-six patients with suspected pulmonary infection were enrolled in the final analysis. All patients received bronchoscopy, and the specimens collected were sent for mNGS on the two different sequencing platforms. Results: The diagnostic sensitivity of the Illumina and BGI platforms was notably higher than that of conventional examination (76.9% vs. 38.5%, p < 0.001; 82.1% vs. 38.5%, p < 0.001; respectively). The sensitivity and specificity for pulmonary infection diagnosis were not significantly different between the Illumina and BGI platforms. Furthermore, the pathogenic detection rate of the two platforms were not significantly different. Conclusion: The Illumina and BGI platforms exhibited similar diagnostic performance for pulmonary infectious diseases using clinical specimens, and both are superior to conventional examinations.
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Affiliation(s)
| | | | | | | | - Yubao Wang
- *Correspondence: Yubao Wang, , Jing Feng,
| | - Jing Feng
- *Correspondence: Yubao Wang, , Jing Feng,
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22
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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] [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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Yu Y, Wang S, Dong G, Niu Y. Diagnostic Performance of Metagenomic Next⁃Generation Sequencing in the Diagnosis of Prosthetic Joint Infection Using Tissue Specimens. Infect Drug Resist 2023; 16:1193-1201. [PMID: 36879851 PMCID: PMC9985395 DOI: 10.2147/idr.s397260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/21/2023] [Indexed: 03/04/2023] Open
Abstract
Purpose The purpose of this study was to evaluate the ability of metagenomic next-generation sequencing (mNGS) diagnosing prosthetic joint infection (PJI) using tissue from hip/knee rapidly and precisely, especially in patients who had received antibiotic treatment within the preceding two weeks. Methods From May 2020 to March 2022, 52 cases with suspected PJI were enrolled. mNGS was performed on surgical tissue samples. The sensitivity and specificity of mNGS in diagnosis was evaluated using culture in conjunction with MSIS criteria. This study also looked at how antibiotic use affected culture and mNGS efficacy. Results According to MSIS criteria, 31 of the 44 cases had PJI, and 13 were classified in the aseptic loosening group. Sensitivity, specificity, positive/negative predictive value (PPV/NPV), positive/negative likelihood ratio (PLR/NLR), and area under the curve (AUC) of mNGS assay were 80.6% (71.9-91.8%), 84.6 (73.7-97.9%), 92.6 (84.2-98.7%), 64.7 (58.6-74.7%), 5.241 (4.081-6.693), 0.229 (0.108-0.482) and 0.826 (0.786-0.967), respectively, with MSIS as a reference. When MSIS was used as a reference, the results of culture assay were 45.2% (40.8-51.5%), 100 (100.0-100.0%), 100 (100.0-100.0%), 43.3 (39.1-49.5%), +∞, 0.548 (0.396-0.617) and 0.726 (0.621-0.864), respectively. The AUC values for mNGS and culture were 0.826 and 0.731, respectively, and the differences were insignificant. mNGS demonstrated higher sensitivity than culture in PJI subjects who had previously received antibiotic treatment within 2 weeks (69.5% vs 23.1%, P = 0.03). Conclusion In our series, mNGS yield a higher sensitivity for diagnosis and pathogen detection of PJI compared to microbiological culture. Additionally, mNGS is less affected by prior antibiotic exposure.
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Affiliation(s)
- Yali Yu
- Department of Clinical Laboratory, Zhengzhou Orthopaedics Hospital, Zhengzhou, People's Republic of China
| | - Shaohua Wang
- Department of Joint Surgery, Zhengzhou Orthopaedics Hospital, Zhengzhou, People's Republic of China
| | - Guixiang Dong
- Department of Clinical Laboratory, Zhengzhou Orthopaedics Hospital, Zhengzhou, People's Republic of China
| | - Yanli Niu
- Laboratory of Cell Signal Transduction, School of Basic Medical Sciences, Henan University, Kaifeng, People's Republic of China
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Liu J, Zhang Q, Dong YQ, Yin J, Qiu YQ. Diagnostic accuracy of metagenomic next-generation sequencing in diagnosing infectious diseases: a meta-analysis. Sci Rep 2022; 12:21032. [PMID: 36470909 PMCID: PMC9723114 DOI: 10.1038/s41598-022-25314-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Many common pathogens are difficult or impossible to detect using conventional microbiological tests. However, the rapid and untargeted nature of metagenomic next-generation sequencing (mNGS) appears to be a promising alternative. To perform a systematic review and meta-analysis of evidence regarding the diagnostic accuracy of mNGS in patients with infectious diseases. An electronic literature search of Embase, PubMed and Scopus databases was performed. Quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. Summary receiver operating characteristics (sROC) and the area under the curve (AUC) were calculated; A random-effects model was used in cases of heterogeneity. A total of 20 papers were eligible for inclusion and synthesis. The sensitivity and specificity of diagnostic mNGS were 75% and 68%, respectively. The AUC from the SROC was 85%, corresponding to excellent performance. mNGS demonstrated satisfactory diagnostic performance for infections and yielded an overall detection rate superior to conventional methods.
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Affiliation(s)
- Jian Liu
- grid.13402.340000 0004 1759 700XDepartment of Intensive Care Unit, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Qiao Zhang
- grid.13402.340000 0004 1759 700XDepartment of Clinical Pharmacy, Zhejiang Provincial Key Laboratory for Drug Evaluation and Clinical Research, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Yong-Quan Dong
- Department of Respiratory Disease, Yinzhou No.2 Hospital, Ningbo, Zhejiang China
| | - Jie Yin
- grid.9227.e0000000119573309Department of Colorectal Medicine, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang China
| | - Yun-Qing Qiu
- grid.13402.340000 0004 1759 700XDepartment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang China
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Patient-Reported Outcome on Quality of Life and Pain after Revision Arthroplasty for Periprosthetic Joint Infection: A Cross-Sectional Study. J Clin Med 2022; 11:jcm11237182. [PMID: 36498756 PMCID: PMC9741318 DOI: 10.3390/jcm11237182] [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: 11/09/2022] [Revised: 11/27/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
This study aims to explore the quality of life (QOL) and pain after revision surgery for periprosthetic joint infection (PJI) based on patients' reported outcomes. A cross-sectional questionnaire survey was conducted and 137 valid responses were included (response rate 64.0%). A total of 42 patients underwent debridement with implant retention (DAIR), 31 underwent one-stage revision, and 64 underwent two-stage revision. The average overall SF-36 score was 70.3. The DAIR group had significantly higher SF-36 than the two-stage revision group (p = 0.01). There was no significant difference between the one-stage revision group and the other two groups. A total of 74.5% of patients reported pain with an average McGill Pain Questionnaire (MPQ) score of 8.6. There was no significant difference in the MPQ scores among the three groups. Simple linear regression analyses demonstrated that higher preoperative PMN%, VAS, and shorter hospital stay were associated with pain (adjusted R2 = 4%, p = 0.020; adjusted R2 = 2.1%, p = 0.048; adjusted R2 = 2.1%, p = 0.049; respectively). We concluded that the overall QOL of patients after revision surgery for PJI is generally satisfactory. Persistent pain is prevalent, but the severity was mostly mild. Preoperative PMN%, VAS, and hospital stay were associated with postoperative pain.
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Shi Y, Wu J, Liu T, Li Y, Liu Y, Gu Y, Qi Y. Analysis of Metagenomic Next-Generation Sequencing Results of 25 Pus Samples. Infect Drug Resist 2022; 15:6515-6524. [DOI: 10.2147/idr.s385925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
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Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: a Multicenter Retrospective Study. Microbiol Spectr 2022; 10:e0247321. [PMID: 35943274 PMCID: PMC9431624 DOI: 10.1128/spectrum.02473-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has been gradually applied to clinical practice due to its unbiased characteristics of pathogen detection. However, its diagnostic performance and clinical value in suspected pulmonary infection need to be evaluated. We systematically reviewed the clinical data of 246 patients with suspected pulmonary infection from 4 medical institutions between January 2019 and September 2021. The diagnostic performances of mNGS and conventional testing (CT) were systematically analyzed based on bronchoalveolar lavage fluid (BALF). The impacts of mNGS and CT on diagnosis modification and treatment adjustment were also assessed. The positive rates of mNGS and CT were 47.97% and 23.17%, respectively. The sensitivity of mNGS was significantly higher than that of CT (53.49% versus 23.26%, P < 0.01), especially for infections of Mycobacterium tuberculosis (67.86% versus 17.86%, P < 0.01), atypical pathogens (100.00% versus 7.14%, P < 0.01), viruses (92.31% versus 7.69%, P < 0.01), and fungi (78.57% versus 39.29%, P < 0.01). The specificity of mNGS was superior to that of CT, with no statistical difference (90.32% versus 77.42%, P = 0.167). The positive predictive value (PPV) and negative predictive value (NPV) of mNGS were 97.46% and 21.88%, respectively. Diagnosis modification and treatment adjustment were conducted in 32 (32/246, 13.01%) and 23 (23/246, 9.35%) cases, respectively, according to mNGS results only. mNGS significantly improved the diagnosis of suspected pulmonary infection, especially infections of M.tuberculosis, atypical pathogens, viruses, and fungi, and it demonstrated the pathogen distribution of pulmonary infections. It is expected to be a promising microbiological detection and diagnostic method in clinical practice. IMPORTANCE Pulmonary infection is a heterogeneous and complex infectious disease with high morbidity and mortality worldwide. In clinical practice, a considerable proportion of the etiology of pulmonary infection is unclear, microbiological diagnosis being challenging. Metagenomic next-generation sequencing detects all nucleic acids in a sample in an unbiased manner, revealing the microbial community environment and organisms and improving the microbiological detection and diagnosis of infectious diseases in clinical settings. This study is the first multicenter, large-scale retrospective study based entirely on BALF for pathogen detection by mNGS, and it demonstrated the superior performance of mNGS for microbiological detection and diagnosis of suspected pulmonary infection, especially in infections of Mycobacterium tuberculosis, atypical pathogens, viruses, and fungi. It also demonstrated the pathogen distribution of pulmonary infections in the real world, guiding targeted treatment and improving clinical management and prognoses.
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Zheng YR, Lin SH, Chen YK, Cao H, Chen Q. Application of metagenomic next-generation sequencing in the detection of pathogens in bronchoalveolar lavage fluid of infants with severe pneumonia after congenital heart surgery. Front Microbiol 2022; 13:954538. [PMID: 35992666 PMCID: PMC9391048 DOI: 10.3389/fmicb.2022.954538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundMetagenomic next-generation sequencing (mNGS) has become a valuable diagnostic tool in clinical etiology detection due to its rapidity, accuracy, and high throughput. However, the role of this technology in the diagnosis and treatment of infants with severe pneumonia after congenital heart surgery is still unclear.MethodsWe conducted a retrospective cohort study of infants with severe pneumonia after congenital heart surgery. Samples were collected from infants in the hospital’s cardiac intensive care unit between January 2010 and January 2022. The conventional microbiological test (CMT) group consisted of patients who underwent routine microbiological examination, and the infants’ bronchoalveolar lavage fluid was examined. The mNGS group consisted of patients who underwent mNGS and routine microbiological examinations.ResultsThe overall positive rate of mNGS was significantly higher than that of CMT (88.4 vs. 62.5%, P = 0.009). After receipt of the microbiological results, 30/43 (70%) patients in the mNGS group had a change in antibiotic use compared with 14/40 (35%) in the CMT group (P = 0.002). Subsequently, after adjusting the treatment plan according to the microbiological test results, the number of people with improved pulmonary infection in the mNGS group was significantly higher than that in the CMT group (63 vs. 28%, P < 0.05). In addition, the duration of invasive ventilation, length of CICU stay and total hospital length of stay in the mNGS group were significantly lower than those in the CMT group (P < 0.05).ConclusionmNGS is a valuable tool to determine the etiology of infants with severe pneumonia after congenital heart disease surgery. It can significantly improve the sensitivity of pathogen detection, which can help determine appropriate antimicrobial drugs, improve the diagnostic accuracy of the disease, and improve outcomes.
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Affiliation(s)
- Yi-Rong Zheng
- Department of Cardiac Surgery, Fujian Branch of Shanghai Children’s Medical Center, Fuzhou, China
- Fujian Children’s Hospital, Fuzhou, China
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Women and Children’s Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Shi-Hao Lin
- Department of Cardiac Surgery, Fujian Branch of Shanghai Children’s Medical Center, Fuzhou, China
- Fujian Children’s Hospital, Fuzhou, China
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Women and Children’s Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Yu-Kun Chen
- Department of Cardiac Surgery, Fujian Branch of Shanghai Children’s Medical Center, Fuzhou, China
- Fujian Children’s Hospital, Fuzhou, China
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Women and Children’s Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Hua Cao
- Department of Cardiac Surgery, Fujian Branch of Shanghai Children’s Medical Center, Fuzhou, China
- Fujian Children’s Hospital, Fuzhou, China
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Women and Children’s Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Qiang Chen
- Department of Cardiac Surgery, Fujian Branch of Shanghai Children’s Medical Center, Fuzhou, China
- Fujian Children’s Hospital, Fuzhou, China
- Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Women and Children’s Critical Diseases Research, Fujian Maternity and Child Health Hospital, Fuzhou, China
- *Correspondence: Qiang Chen,
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Fang X, Cai Y, Chen X, Huang C, Lin Y, Huang Z, Zhang C, Huang Y, Li W, Zhang W. The role of metagenomic next-generation sequencing in the pathogen detection of invasive osteoarticular infection. Int J Infect Dis 2022; 122:996-1001. [PMID: 35908720 DOI: 10.1016/j.ijid.2022.07.061] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/19/2022] [Accepted: 07/24/2022] [Indexed: 10/16/2022] Open
Abstract
OBJECTIVE This study aimed to analyzed the pathogenic bacteria spectrum in invasive and primary osteoarticular infection (IOI and POI), and compared the pathogen detection rate of metagenomic next-generation sequencing (mNGS) and microbial culture in IOI and POI. METHODS The suspected POI and IOI cases from 2008 to 2021 were included. The diagnosis of POI or IOI were made by at least two orthopaedic surgeons, two infectious diseases specialist and one senior microbiologist. Demographic characteristics, microbial culture results and so on were recorded. The pathogenic bacteria spectrum in IOI and POI were analyzed and the ability of mNGS and microbial culture in pathogen detection in IOI and POI were compared. RESULTS There were 63 POI cases and 92 cases, the common pathogen in POI and IOI were both Staphylococcus aureus. There are more cases with negative microbial culture results and multiple infections in IOI, and many cases were caused by rare and fastidious bacteria. The introduction of the mNGS could significantly increase the pathogen detection rate to 92.39% in IOI, which was 8.69% higher than that of microbial culture (P=0.007), while the improvement in POI was limited to about 2%. CONCLUSIONS mNGS was an ideal tool for IOI pathogen detection.
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Affiliation(s)
- Xinyu Fang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Yuanqing Cai
- Department of Orthopaedic Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Xiaoqing Chen
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China; Department of Orthopaedic Surgery, Quanzhou First Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China.
| | - Changyu Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Yiming Lin
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Zida Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Chaofan Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Ying Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Wenbo Li
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
| | - Wenming Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
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30
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Liang M, Fan Y, Zhang D, Yang L, Wang X, Wang S, Xu J, Zhang J. Metagenomic next-generation sequencing for accurate diagnosis and management of lower respiratory tract infections. Int J Infect Dis 2022; 122:921-929. [PMID: 35908723 DOI: 10.1016/j.ijid.2022.07.060] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/07/2022] [Accepted: 07/23/2022] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in patients with suspected lower respiratory tract infections (LRTIs). METHODS This retrospective study reviewed patients with suspected LRTIs in Wuhan Union Hospital. Data including demographic, laboratory, and radiological profiles; treatment; and outcomes were recorded and analyzed. RESULTS mNGS identified pathogenic microbes in 100/140 (71.4%) patients, although 135 (96.4%) had received empiric antibiotic treatment before the mNGS tests. Single bacterial infection (35/100, 35%) was the most common type of infection in patients with positive mNGS results, followed by single fungal infection (14/100, 14%), bacterial-viral co-infection (14/100, 14%), single viral infection (12/100, 12%), bacterial-fungal co-infection (9/100, 9%), fungal-viral co-infection (9/100, 9%), and bacterial-fungal-viral co-infection (7/100, 7%). Moreover, compared with culture test, mNGS showed higher sensitivity (63/85, 74.1% vs. 22/85, 25.9% P=0.001) and lower processing time (24 h vs 48 h). Antibiotic treatment was adjusted or confirmed based on the mNGS results in 123 (87.9%) patients, including 5 (3.6%), 33 (23.6%) and 85 (60.7%) patients in whom treatment was downgraded, upgraded and unchanged, respectively, and almost all patients, regardless of escalation, de-escalation, or no change in treatment, showed significant improvement in clinical symptoms and inflammatory indicators. Additionally, 17 (12.1%) patients were referred to Wuhan Pulmonary Hospital for further treatment because of confirmed or suspected tuberculosis. CONCLUSIONS mNGS could be a promising technique for microbiological diagnosis and antibiotic management, potentially improving outcomes of patients.
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Affiliation(s)
- Mengyuan Liang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Yamin Fan
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Dongmei Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Lian Yang
- Department of Radiology, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Xiaorong Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Sufei Wang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
| | - Juanjuan Xu
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China.
| | - Jianchu Zhang
- Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical Collage, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China.
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Wu W, Jiang H, Zhang Y, Zhou Y, Bai G, Shen L, Zhou H, Chen X, Hu L. Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Secondary Glaucoma in Patients With Cytomegalovirus-Induced Corneal Endotheliitis. Front Microbiol 2022; 13:940818. [PMID: 35865935 PMCID: PMC9295740 DOI: 10.3389/fmicb.2022.940818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
Glaucoma is the second leading cause of blindness globally. Growing scientific evidence indicated that inflammation of the trabecular meshwork induced by corneal endotheliitis could lead to secondary glaucoma. Cytomegalovirus (CMV) has been identified as the most common herpes virus in corneal endotheliitis patients. Early detection is critical in preventing endothelial cell loss, and patient management should vary based on different pathological factors. However, routine culture and real-time polymerase chain reaction (qPCR) have difficult in distinguishing whether CMV, Varicella Zoster Virus (VZV) or Herpes Simplex Virus (HSV) causes endothiliitis. This may result in inappropriate treatment, which may prolong or aggravate the status of disease. We compared the sensitivity and specificity of qPCR and Metagenomic Next-Generation Sequencing (mNGS) in the aqueous humor of patients with suspected CMV endotheliitis in this study. Our results showed that four out of 11 (36.4%) of our patients were positive for CMV by qPCR, whereas mNGS had a 100% detection rate of CMV. Our findings implied that mNGS could be a useful diagnostic tool for CMV-induced endotheliitis.
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Affiliation(s)
- Wei Wu
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hua Jiang
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Zhang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yang Zhou
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd., Hangzhou, China
| | - Guannan Bai
- The Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingwei Shen
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Hongwei Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangjun Chen
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Lab of Ophthalmology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Xiangjun Chen,
| | - Lidan Hu
- The Children’s Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China
- Lidan Hu,
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Tan J, Liu Y, Ehnert S, Nüssler AK, Yu Y, Xu J, Chen T. The Effectiveness of Metagenomic Next-Generation Sequencing in the Diagnosis of Prosthetic Joint Infection: A Systematic Review and Meta-Analysis. Front Cell Infect Microbiol 2022; 12:875822. [PMID: 35755833 PMCID: PMC9226560 DOI: 10.3389/fcimb.2022.875822] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
Background A prosthetic joint infection (PJI) is a devastating complication following total joint arthroplasties with poor prognosis. Identifying an accurate and prompt diagnostic method is particularly important for PJI. Recently, the diagnostic value of metagenomic next-generation sequencing (mNGS) in detecting PJI has attracted much attention, while the evidence of its accuracy is quite limited. Thus, this study aimed to evaluate the accuracy of mNGS for the diagnosis of PJI. Methods We summarized published studies to identify the potential diagnostic value of mNGS for PJI patients by searching online databases using keywords such as “prosthetic joint infection”, “PJI”, and “metagenomic sequencing”. Ten of 380 studies with 955 patients in total were included. The included studies provided sufficient data for the completion of 2-by-2 tables. We calculated the sensitivity, specificity, and area under the SROC curve (AUC) to evaluate mNGS for PJI diagnosis. Results We found that the pooled diagnostic sensitivity and specificity of mNGS for PJI were 0.93 (95% CI, 0.83 to 0.97) and 0.95 (95% CI, 0.92 to 0.97), respectively. Positive and negative likelihood ratios were 18.3 (95% CI, 10.9 to 30.6) and 0.07 (95% CI, 0.03 to 0.18), respectively. The area under the curve was 0.96 (95% CI, 0.93 to 0.97). Conclusion Metagenomic next-generation sequencing displays high accuracy in the diagnosis of PJI, especially for culture-negative cases.
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Affiliation(s)
- Jun Tan
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yang Liu
- Department of Clinical Sciences, Orthopedics, Faculty of Medicine, Lund University, Lund, Sweden
| | - Sabrina Ehnert
- Department of Trauma and Reconstructive Surgery, BG Trauma Center Tübingen, Siegfried Weller Institute for Trauma Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Andreas K Nüssler
- Department of Trauma and Reconstructive Surgery, BG Trauma Center Tübingen, Siegfried Weller Institute for Trauma Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Yang Yu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianzhong Xu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tao Chen
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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The DendrisCHIP® Technology as a New, Rapid and Reliable Molecular Method for the Diagnosis of Osteoarticular Infections. Diagnostics (Basel) 2022; 12:diagnostics12061353. [PMID: 35741163 PMCID: PMC9222036 DOI: 10.3390/diagnostics12061353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022] Open
Abstract
Osteoarticular infections are major disabling diseases that can occur after orthopedic implant surgery in patients. The management of these infections is very complex and painful, requiring surgical intervention in combination with long-term antibiotic treatment. Therefore, early and accurate diagnosis of the causal pathogens is essential before formulating chemotherapeutic regimens. Although culture-based microbiology remains the most common diagnosis of osteoarticular infections, its regular failure to identify the causative pathogen as well as its long-term modus operandi motivates the development of rapid, accurate, and sufficiently comprehensive bacterial species-specific diagnostics that must be easy to use by routine clinical laboratories. Based on these criteria, we reported on the feasibility of our DendrisCHIP® technology using DendrisCHIP®OA as an innovative molecular diagnostic method to diagnose pathogen bacteria implicated in osteoarticular infections. This technology is based on the principle of microarrays in which the hybridization signals between oligoprobes and complementary labeled DNA fragments from isolates queries a database of hybridization signatures corresponding to a list of pre-established bacteria implicated in osteoarticular infections by a decision algorithm based on machine learning methods. In this way, this technology combines the advantages of a PCR-based method and next-generation sequencing (NGS) while reducing the limitations and constraints of the two latter technologies. On the one hand, DendrisCHIP®OA is more comprehensive than multiplex PCR tests as it is able to detect many more germs on a single sample. On the other hand, this method is not affected by the large number of nonclinically relevant bacteria or false positives that characterize NGS, as our DendrisCHIP®OA has been designed to date to target only a subset of 20 bacteria potentially responsible for osteoarticular infections. DendrisCHIP®OA has been compared with microbial culture on more than 300 isolates and a 40% discrepancy between the two methods was found, which could be due in part but not solely to the absence or poor identification of germs detected by microbial culture. We also demonstrated the reliability of our technology in correctly identifying bacteria in isolates by showing a convergence (i.e., same bacteria identified) with NGS superior to 55% while this convergence was only 32% between NGS and microbial culture data. Finally, we showed that our technology can provide a diagnostic result in less than one day (technically, 5 h), which is comparatively faster and less labor intensive than microbial cultures and NGS.
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Mo F, Zhang P, Li Q, Yang X, Ma J, Zhang J. Development and Evaluation of a Film Forming System Containing Myricetin and Miconazole Nitrate for Preventing Candida albicans Catheter-Related Infection. Microb Drug Resist 2022; 28:468-483. [PMID: 35451882 DOI: 10.1089/mdr.2021.0242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Candida albicans catheter-related infection (CRI) is a great challenge in clinic now, mainly due to the difficulty in eradicating the biofilms. Purpose: In this study, the mechanism of the antibiofilm effect of myricetin (MY) on C. albicans was illustrated. A film forming system (FFS) containing MY and miconazole nitrate (MN) was developed, optimized, and evaluated. The anti-infection effect of MY+MN@FFS against C. albicans CRI was investigated in vivo. Study Design and Methods: To clarify the mechanism of the action of MY, the influence of MY on each key process of the formation of C. albicans biofilms was evaluated. To deliver MY and MN into the skin and form a drug reservoir on the surface of the skin, the FFS was used as a carrier and MY+MN@FFS was developed, optimized, and evaluated. After preliminary confirmation of drug safety, a percutaneously inserted C. albicans CRI mouse model was established to investigate the in vivo anti-infection effect of MY+MN@FFS by fluorescence microscopy and scanning electron microscopy on the outer surface of the catheters, hematoxylin/eosin staining, and periodic acid-Schiff staining of the mice skin tissues. Results: MY was found to inhibit the morphological transition of C. albicans and the secretion of exopolysaccharides, resulting in a reduction in biofilms. MY+MN@FFS exhibited excellent properties and no irritation to mice skin. In an in vivo anti-infection study, MY+MN@FFS exhibited an excellent preventive effect against percutaneously inserted C. albicans CRI. Conclusion: MY+MN@FFS might be a potential approach for effectively preventing percutaneously inserted C. albicans CRI in clinic.
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Affiliation(s)
- Fei Mo
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Peipei Zhang
- Biobank, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P. R. China
| | - Qingqing Li
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xianwei Yang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Jia Ma
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Jiye Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, P.R. China
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Septic Failure After One-Stage Exchange for Prosthetic Joint Infection of the Hip: Microbiological Implications. J Arthroplasty 2022; 37:373-378. [PMID: 34740790 DOI: 10.1016/j.arth.2021.10.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/30/2021] [Accepted: 10/26/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The microbiological implications of septic failure after 1-stage exchange for prosthetic joint infection (PJI) of the hip remain unclear. METHODS Information was gathered on comorbidities, previous procedures, preoperative and postoperative microbiology results, methods of detection, and antibiotic resistance patterns, for all patients, who developed septic failure after 1-stage exchange for PJI of the hip performed at our institution during 2001-2017. RESULTS Seventy-seven patients were identified. Septic failure was diagnosed a mean of 1.7 (standard deviation 2.3, range 0-11.8) years later. Although the spectrum of microorganisms was similar to preoperative, in the majority of patients (55%), the initial microorganism(s) was (were) replaced by (a) totally different microorganism(s). Overall, there was a decrease in the number of polymicrobial PJIs. The number of patients with high virulent microorganisms decreased significantly from 52 to 36 (P = .034). The number of PJIs due to gram-negative pathogens remained similar (11 vs 14, P = .491). The number of rifampicin-resistant staphylococci, fluoroquinolone-resistant streptococci, enterococci, and fungi changed from 8 to 15, 0 to 2, 7 to 3, and 1 to 2, respectively, but these changes did not reach statistical significance. CONCLUSION The majority of reinfections is caused by different infecting bacteria, hence it is essential to perform a new diagnostic workup and not base treatment decisions (solely) on historical cultures. We were furthermore unable to irrefutably prove that, from a microbiological point of view, septic failure after 1-stage exchange comes with increased challenges. Given the time interval to failure, we propose that a longer follow-up of these patients is needed, than previously suggested.
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Miller S, Chiu C. The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis. Clin Chem 2021; 68:115-124. [PMID: 34969106 DOI: 10.1093/clinchem/hvab173] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) for pathogen detection is becoming increasingly available as a method to identify pathogens in cases of suspected infection. mNGS analyzes the nucleic acid content of patient samples with high-throughput sequencing technologies to detect and characterize microorganism DNA and/or RNA. This unbiased approach to organism detection enables diagnosis of a broad spectrum of infection types and can identify more potential pathogens than any single conventional test. This can lead to improved ability to diagnose patients, although there remains concern regarding contamination and detection of nonclinically significant organisms. CONTENT We describe the laboratory approach to mNGS testing and highlight multiple considerations that affect diagnostic performance. We also summarize recent literature investigating the diagnostic performance of mNGS assays for a variety of infection types and recommend further studies to evaluate the improvement in clinical outcomes and cost-effectiveness of mNGS testing. SUMMARY The majority of studies demonstrate that mNGS has sensitivity similar to specific PCR assays and will identify more potential pathogens than conventional methods. While many of these additional organism detections correlate with the expected pathogen spectrum based on patient presentations, there are relatively few formal studies demonstrating whether these are true-positive infections and benefits to clinical outcomes. Reduced specificity due to contamination and clinically nonsignificant organism detections remains a major concern, emphasizing the importance of careful interpretation of the organism pathogenicity and potential association with the clinical syndrome. Further research is needed to determine the possible improvement in clinical outcomes and cost-effectiveness of mNGS testing.
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Affiliation(s)
- Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
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Edward P, Handel AS. Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis: A Review of the Literature With a Focus on Pediatrics. J Pediatric Infect Dis Soc 2021; 10:S71-S77. [PMID: 34951466 DOI: 10.1093/jpids/piab104] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metagenomic next-generation sequencing (mNGS) is a novel tool for identifying microbial DNA and/or RNA in blood and other clinical specimens. In the face of increasingly complex patients and an ever-growing list of known potential pathogens, mNGS has been proposed as a breakthrough tool for unbiased pathogen identification. Studies have begun to explore the clinical applicability of mNGS in a variety of settings, including endocarditis, pneumonia, febrile neutropenia, osteoarticular infections, and returning travelers. The real-world impact of mNGS has also been assessed through retrospective studies, documenting varying degrees of success and limitations. In this review, we will explore current highlights of the clinical mNGS literature, with a focus on pediatric data where available. We aim to provide the reader with a deeper understanding of the strengths and weaknesses of mNGS and to provide direction toward areas requiring further research.
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Affiliation(s)
- Priya Edward
- Department of Pediatrics, Division of Infectious Diseases, Lurie Children's Hospital, Chicago, Illinois, USA
| | - Andrew S Handel
- Department of Pediatrics, Division of Infectious Diseases, Stony Brook Children's Hospital, Stony Brook, New York, USA
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Tang Y, Zhao D, Wang S, Yi Q, Xia Y, Geng B. Diagnostic Value of Next-Generation Sequencing in Periprosthetic Joint Infection: A Systematic Review. Orthop Surg 2021; 14:190-198. [PMID: 34935279 PMCID: PMC8867422 DOI: 10.1111/os.13191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 11/11/2021] [Accepted: 11/19/2021] [Indexed: 01/03/2023] Open
Abstract
Next‐generation sequencing (NGS) has developed rapidly in the last decade and is emerging as a promising diagnostic tool for periprosthetic joint infection (PJI). However, its diagnostic value for PJI is still uncertain. This systematic review aimed to explore the diagnostic value of NGS for PJI and verify its accuracy for culture‐negative PJI patients. We conducted this systematic review in accordance with the Preferred Reporting Items for Systematic Reviews and Meta‐Analysis (PRISMA) guidelines. Medline, Embase, and Cochrane Library were searched to identify diagnostic technique studies evaluating the accuracy of NGS in the diagnosis of PJI. The diagnostic sensitivity, specificity, and positive and negative predictive values were estimated for each article. The detection rate of NGS for culture‐negative PJI patients or PJI patients with antibiotic administration history was also calculated. Of the 87 identified citations, nine studies met the inclusion criteria. The diagnostic sensitivities and specificities of NGS ranged from 63% to 96% and 73% to 100%, respectively. The positive and negative predictive values ranged from 71% to 100% and 74% to 95%, respectively. The detection rate of NGS for culture‐negative PJI patients in six studies was higher than 50% (range from 82% to 100%), while in three studies it was lower than 50% (range from 9% to 31%). Also, the detection rate of NGS for PJIs with antibiotic administration history ranged from 74.05% to 92.31%. In conclusion, this systematic review suggests that NGS may have the potential to be a new tool for the diagnosis of PJI and should be considered to be added to the portfolio of diagnostic procedures. Furthermore, NGS showed a favorable diagnostic accuracy for culture‐negative PJI patients or PJI patients with antibiotic administration history. However, due to the small sample sizes of studies and substantial heterogeneity among the included studies, more research is needed to confirm or disprove these findings.
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Affiliation(s)
- Yuchen Tang
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Dacheng Zhao
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Shenghong Wang
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Qiong Yi
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Yayi Xia
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
| | - Bin Geng
- Department of Orthopaedics, Lanzhou University Second Hospital, Orthopaedic Key Laboratory of Gansu Province, Orthopaedic Clinical Research Center of Gansu Province, Lanzhou, China
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Fang X, Wang Q, Yang X, Zhang F, Huang C, Huang Z, Shen H, Zhang W. What is the appropriate extended duration of antibiotic prophylaxis after two-stage revision for chronic PJI? Bone Joint Res 2021; 10:790-796. [PMID: 34894718 PMCID: PMC8696522 DOI: 10.1302/2046-3758.1012.bjr-2021-0225.r1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aims To explore the effect of different durations of antibiotics after stage II reimplantation on the prognosis of two-stage revision for chronic periprosthetic joint infection (PJI). Methods This study involved a retrospective collection of patients who underwent two-stage revision for chronic PJI and continued to use extended antibiotic prophylaxis in two regional medical centres from January 2010 to June 2018. The patients were divided into a short (≤ one month) or a long (> one month) course of treatment based on the duration of antibiotics following stage II reimplantation. The difference in the infection control rate between the two groups was compared, and prognostic factors for recurrence were analyzed. Results A total of 105 patients with chronic PJI were enrolled: 64 patients in the short course group and 41 patients in the long course group. For 99 of the patients, the infection was under control during a follow-up period of at least 24 months after two-stage revision. For the short course group, the mean duration of antibiotic prophylaxis after stage II reimplantation was 20.17 days (SD 5.30) and the infection control rate was 95.3%; for the long course group these were 45.02 days (SD 15.03) and 92.7%, respectively. There was no significant difference in infection control rates between the two groups (p = 0.676). Cox regression analysis found that methicillin-resistant staphylococcus infection (p = 0.015) was an independent prognostic factor for recurrence. Conclusion After stage II reimplantation surgery of two-stage revision for chronic PJI, extended antibiotic prophylaxis for less than one month can achieve good infection control rate. Cite this article: Bone Joint Res 2021;10(12):790–796.
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Affiliation(s)
- Xinyu Fang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Qiaojie Wang
- Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Xurong Yang
- Department of Orthopaedic Surgery, Jiangle County General Hospital, Sanming, China
| | - Feiyang Zhang
- Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Changyu Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Hao Shen
- Department of Orthopaedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Wenming Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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Zhang Y, Xu H, Liu Y, Kang J, Chen H, Wang Z, Cai D. Case Report: Fascioliasis Hepatica Precisely Diagnosed by Metagenomic Next-Generation Sequencing and Treated With Albendazole. Front Med (Lausanne) 2021; 8:773145. [PMID: 34901089 PMCID: PMC8651557 DOI: 10.3389/fmed.2021.773145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
The clinical manifestations of fascioliasis hepatica in humans are unspecific. Traditional diagnosis relies on evidence of live parasites or eggs in the bile or feces. However, due to similar imaging manifestations, they are often misdiagnosed as malignant tumors. Here, we report a case of a 43-year-old woman with fever and space-occupying liver disease. Liver biopsy, parasite-specific antibody screening, and stool testing did not find any pathogens. Therefore, metagenomic next-generation sequencing (mNGS) and routine microbiological examinations were performed. Finally, Fasciola hepatica was only identified by mNGS. The body temperature of the patient and the eosinophil count remained normal, and the space-occupying liver lesions were significantly absorbed after more than 7 months of treatment with albendazole. The details of this case highlight the timely use of mNGS to identify parasites and judge therapeutic effects after treatment, providing important help for clinical decision-making.
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Affiliation(s)
- Yaling Zhang
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Huan Xu
- Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Yi Liu
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Kang
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hairu Chen
- Vision Medicals Center for Infection Diseases, Guangzhou, China
| | - Zhiyi Wang
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dachuan Cai
- Department of Infectious Diseases, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Cai S, Yang Y, Pan J, Miao Q, Jin W, Ma Y, Zhou C, Gao X, Wang C, Hu B. The clinical value of valve metagenomic next-generation sequencing when applied to the etiological diagnosis of infective endocarditis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1490. [PMID: 34805352 PMCID: PMC8573444 DOI: 10.21037/atm-21-2488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/04/2021] [Indexed: 12/22/2022]
Abstract
Background Metagenomic next-generation sequencing (mNGS) is widely applied in the etiological diagnosis of infectious diseases. However, the clinical practice of mNGS in infective endocarditis (IE) is relatively less studied. This research aimed to assess the etiological diagnostic value of valve mNGS in IE. Methods We retrospectively analyzed 49 IE patients who underwent cardiac valve surgery in Zhongshan Hospital, Fudan University, Shanghai from 1 June 2018 to 30 November 2020. Among these IE patients, 28 were culture positive and 21 were culture negative. The culture results of the culture-positive IE patients were set as gold standard to assess the sensitivity and specificity of valve mNGS in the etiological diagnosis of IE. We studied the positive detection rate of pathogens by valve mNGS among the culture-negative IE patients. During the same period, we also collected the resected valves of 8 patients with non-infective valvular diseases for mNGS as negative controls. Results The valve mNGS results of the culture-positive IE patients were the exact same as their culture results. Both the sensitivity and specificity of valve mNGS were 100%. The positive detection rate of pathogens by valve mNGS was 100% among the culture-negative IE patients. The stringent mapped reads number of genera (SMRNG), relative abundance of genera, stringent mapped reads number of species (SMRN), relative abundance of species, and coverage rate of valve mNGS results were significantly higher in culture-positive IE participants than in culture-negative IE participants. The valve mNGS results of the 8 participants with non-infective valvular diseases were all negative. Conclusions Valve mNGS is a promising technology for the etiological diagnosis of IE, especially culture-negative IE, and it may be used to guide precise antibiotic treatment after surgery.
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Affiliation(s)
- Sishi Cai
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ye Yang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jue Pan
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qing Miao
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenting Jin
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuyan Ma
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunmei Zhou
- Department of Microbiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Gao
- Department of Hospital Infection Management, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunsheng Wang
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, 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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42
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Ribeiro VST, Cieslinski J, Bertol J, Schumacher AL, Telles JP, Tuon FF. Detecção de microrganismos em dispositivos ortopédicos sonicados clínicos usando cultura convencional e qPCR. Rev Bras Ortop 2021; 57:689-696. [PMID: 35966434 PMCID: PMC9365468 DOI: 10.1055/s-0041-1732386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/19/2021] [Indexed: 11/20/2022] Open
Abstract
Objective
To evaluate the sensitivity and specificity of the quantitative real-time polymerase chain reaction (qPCR) for
16S rDNA
gene screening using sonicated fluid from orthopedic implants.
Methods
A retrospective study was conducted on 73 sonicated fluids obtained from patients with infection associated with orthopedic implants. The samples were subjected to conventional culture and molecular testing using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and qPCR for
16S rDNA
. The cycle threshold values were used to define a cut-off of the qPCR of the
16S rDNA
for negative and positive cultures.
Results
No statistical differences were observed between the positive and negative culture groups based on the time from the first surgery to infection (
p
= 0.958), age (
p =
0.269), or general comorbidities. Nevertheless, a statistical difference was found between the mean duration of antibiotic use before device removal (3.41 versus 0.94;
p =
0.016). Bacterial DNA was identified in every sample from the sonicated fluids. The median cycle thresholds of the positive and negative cultures were of 25.6 and 27.3 respectively (
p
< 0.001). As a diagnostic tool, a cycle threshold cut-off of 26.89 demonstrated an area under the curve of the receiver operating characteristic of 0.877 (
p
≤ 0.001).
Conclusion
The presence of antimicrobial agents for more than 72 hours decreased culture positivity, but did not influence the qPCR results. Despite this, amplification of the
16S rDNA
may overestimate infection diagnosis.
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Affiliation(s)
- Victoria Stadler Tasca Ribeiro
- Laboratório de Doenças Infecciosas Emergentes (LEID), Escola de Medicina, Departamento de Ciências da Saúde, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, PR, Brasil
| | - Juliette Cieslinski
- Laboratório de Doenças Infecciosas Emergentes (LEID), Escola de Medicina, Departamento de Ciências da Saúde, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, PR, Brasil
| | - Julia Bertol
- School of Medicine, Department of Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, PR, Brasil
| | - Ana Laura Schumacher
- School of Medicine, Department of Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, PR, Brasil
| | - João Paulo Telles
- School of Medicine, Department of Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, PR, Brasil
| | - Felipe Francisco Tuon
- Laboratório de Doenças Infecciosas Emergentes (LEID), Escola de Medicina, Departamento de Ciências da Saúde, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, PR, Brasil
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43
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Hodges NA, Sussman EM, Stegemann JP. Aseptic and septic prosthetic joint loosening: Impact of biomaterial wear on immune cell function, inflammation, and infection. Biomaterials 2021; 278:121127. [PMID: 34564034 DOI: 10.1016/j.biomaterials.2021.121127] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 12/17/2022]
Abstract
The success of total joint replacements has led to consistent growth in the use of arthroplasty in progressively younger patients. However, more than 10 percent of patients require revision surgeries due to implant failure caused by osteolytic loosening. These failures are classified as either aseptic or septic and are associated with the presence of particulate wear debris generated by mechanical action between implant components. Aseptic loosening results from chronic inflammation caused by activation of resident immune cells in contact with implant wear debris. In contrast, septic loosening is defined by the presence of chronic infection at the implant site. However, recent findings suggest that subclinical biofilms may be overlooked when evaluating the cause of implant failure, leading to a misdiagnosis of aseptic loosening. Many of the inflammatory pathways contributing to periprosthetic joint infections are also involved in bone remodeling and resorption. In particular, wear debris is increasingly implicated in the inhibition of the innate and adaptive immune response to resolve an infection or prevent hematogenous spread. This review examines the interconnectivity of wear particle- and infection-associated mechanisms of implant loosening, as well as biomaterials-based strategies to combat infection-related osteolysis.
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Affiliation(s)
- Nicholas A Hodges
- University of Michigan, Department of Biomedical Engineering, Ann Arbor, MI, 48109, USA; Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, FDA, Silver Spring, MD, 20993, USA.
| | - Eric M Sussman
- Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, FDA, Silver Spring, MD, 20993, USA.
| | - Jan P Stegemann
- University of Michigan, Department of Biomedical Engineering, Ann Arbor, MI, 48109, USA.
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44
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Gamie Z, Karthikappallil D, Gamie E, Stamiris S, Kenanidis E, Tsiridis E. Molecular sequencing technologies in the diagnosis and management of prosthetic joint infections. Expert Rev Mol Diagn 2021; 22:603-624. [PMID: 33641572 DOI: 10.1080/14737159.2021.1894929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Prosthetic joint infections (PJIs) can be challenging to eradicate and have high morbidity and mortality. Current microbiology culture methods can be associated with a high false-negative rate of up to 50%. Early and accurate diagnosis is crucial for effective treatment, and negative results have been linked to a greater rate of reoperation. AREAS COVERED There has been increasing investigation of the use of next-generation sequencing (NGS) technology such as metagenomic shotgun sequencing to help identify causative organisms and decrease the uncertainty around culture-negative infections. The clinical importance of the organisms detected and their management, however, requires further study. The polymerase chain reaction (PCR) has shown promise, but in recent years multiple studies have reported similar or lower sensitivity for bacteria detection in PJIs when compared to traditional culture. Furthermore, issues such as high cost and complexity of sample preparation and data analysis are to be addressed before it can move further toward routine clinical practice. EXPERT OPINION Metagenomic NGS has shown results that inspire cautious optimism - both in culture-positive and culture-negative cases of joint infection. Refinement of technique could revolutionize the way PJIs are diagnosed, managed, and drastically improve outcomes from this currently devastating complication.
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Affiliation(s)
- Zakareya Gamie
- Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK; Genomic Medicine - St George's, University of London, Cranmer Terrace, Tooting, London, SW17 0RE; King's College London, Strand, London
| | - Dileep Karthikappallil
- Department of Trauma and Orthopedics, East Cheshire NHS Trust, Macclesfield District General Hospital, Victoria Road, Macclesfield, Cheshire, SK10 3BL, UK
| | - Emane Gamie
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; MBiol, BSc Biological Sciences, University of Leeds Alumni, UK
| | - Stavros Stamiris
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
| | - Eustathios Kenanidis
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
| | - Eleftherios Tsiridis
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
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Xie G, Zhao B, Wang X, Bao L, Xu Y, Ren X, Ji J, He T, Zhao H. Exploring the Clinical Utility of Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infection. Infect Dis Ther 2021; 10:1419-1435. [PMID: 34117999 PMCID: PMC8322361 DOI: 10.1007/s40121-021-00476-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION We aimed to explore the real-world clinical application value and challenges of metagenomic next-generation sequencing (mNGS) for pulmonary infection diagnosis. METHODS We retrospectively reviewed the results of mNGS and conventional tests from 140 hospitalized patients with suspected pulmonary infections from January 2019 to December 2020. The sample types included bronchoalveolar lavage fluid, lung tissue by transbronchial lung biopsy, pleural effusion, blood, and bronchial sputum. Apart from the mNGS reports that our patients received, an extra comprehensive and thorough literature search was conducted. RESULTS Significant differences were noticed in the positive detection rates of pathogens between mNGS and conventional diagnostic testing (115/140, 82.14% vs 50/140, 35.71%, P < 0.05). The percentage of mNGS-positive patients was significantly higher than that of conventional testing-positive patients with regard to bacterial detection (P < 0.01), but no significant differences were found with regard to fungal detection (P = 0.67). Significant statistical differences were found between mixed infection cases (15, 22.70%) and single infection cases (4, 7.84%) in terms of diabetes (P = 0.03). The most frequent pattern of mixed infection was bacteria and fungi mixed infection (40, 40/89 = 44.94%), followed by bacteria mixed infection (29, 29/89 = 32.58%). The sensitivity of mNGS in pulmonary infection diagnosis was much higher than that of conventional test (89.17% vs 50.00%; P < 0.01), but the specificity was the opposite (75.00% vs 81.82%; P > 0.05). CONCLUSION mNGS is a valuable tool for the detection of pulmonary infections, especially mixed pulmonary infections. The most common combinations we found were bacterial-fungal coinfection and bacterial-bacterial coinfection. Still, there are many challenges in the clinical application of mNGS in the diagnosis of pulmonary infections. There is still a lot of work to be done in interpreting the mNGS reports, because both clinical judgment and literature analysis strategy need to be refined.
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Affiliation(s)
- Guijuan Xie
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Bo Zhao
- Affiliated Wuxi Clinical College of Nantong University, Wuxi, China.,Department of Gastroenterology, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China
| | - Xun Wang
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Liang Bao
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Yiming Xu
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Xian Ren
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Jiali Ji
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Ting He
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China.,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China
| | - Hongqing Zhao
- Department of Respiratory, The Affiliated Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, China. .,Affiliated Wuxi Clinical College of Nantong University, Wuxi, China.
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46
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Prosthetic hip joint infection by Bacillus Calmette-Guerin therapy following intravesical instillation for bladder cancer identified using whole-genome sequencing: a case report. BMC Infect Dis 2021; 21:151. [PMID: 33546627 PMCID: PMC7866480 DOI: 10.1186/s12879-021-05831-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Joint replacement is an effective intervention and prosthetic joint infection (PJI) is one of the most serious complications of such surgery. Diagnosis of PJI is often complex and requires multiple modalities of investigation. We describe a rare cause of PJI which highlights these challenges and the role of whole-genome sequencing to achieve a rapid microbiological diagnosis to facilitate prompt and appropriate management. CASE PRESENTATION A 79-year-old man developed chronic hip pain associated with a soft-tissue mass, fluid collection and sinus adjacent to his eight-year-old hip prosthesis. His symptoms started after intravesical Bacillus Calmette-Guerin (BCG) therapy for bladder cancer. Synovasure™ and 16S polymerase chain reaction (PCR) tests were negative, but culture of the periarticular mass and genome sequencing diagnosed BCG infection. He underwent a two-stage joint revision and a prolonged duration of antibiotic therapy which was curative. CONCLUSIONS BCG PJI after therapeutic exposure can have serious consequences, and awareness of this potential complication, identified from patient history, is essential. In addition, requesting appropriate testing is required, together with recognition that traditional diagnostics may be negative in non-pyogenic PJI. Advanced molecular techniques have a role to enhance the timely management of these infections.
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47
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Fang X, Zhang L, Cai Y, Huang Z, Li W, Zhang C, Yang B, Lin J, Wahl P, Zhang W. Effects of different tissue specimen pretreatment methods on microbial culture results in the diagnosis of periprosthetic joint infection. Bone Joint Res 2021; 10:96-104. [PMID: 33517765 PMCID: PMC7937541 DOI: 10.1302/2046-3758.102.bjr-2020-0104.r3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Aims Microbiological culture is a key element in the diagnosis of periprosthetic joint infection (PJI). However, cultures of periprosthetic tissue do not have optimal sensitivity. One of the main reasons for this is that microorganisms are not released from the tissues, either due to biofilm formation or intracellular persistence. This study aimed to optimize tissue pretreatment methods in order to improve detection of microorganisms. Methods From December 2017 to September 2019, patients undergoing revision arthroplasty in a single centre due to PJI and aseptic failure (AF) were included, with demographic data and laboratory test results recorded prospectively. Periprosthetic tissue samples were collected intraoperatively and assigned to tissue-mechanical homogenization (T-MH), tissue-manual milling (T-MM), tissue-dithiothreitol (T-DTT) treatment, tissue-sonication (T-S), and tissue-direct culture (T-D). The yield of the microbial cultures was then analyzed. Results A total of 46 patients were enrolled, including 28 patients in the PJI group and 18 patients in the AF group. In the PJI group, 23 cases had positive culture results via T-MH, 22 cases via T-DTT, 20 cases via T-S, 15 cases via T-MM, and 13 cases via T-D. Three cases under ongoing antibiotic treatment remained culture-negative. Five tissue samples provided the optimal yield. Any ongoing antibiotic treatment had a relevant influence on culture sensitivity, except for T-DTT. Conclusion T-MH had the highest sensitivity. Combining T-MH with T-DTT, which requires no special equipment, may effectively improve bacterial detection in PJI. A total of five periprosthetic tissue biopsies should be sampled in revision arthroplasty for optimal detection of PJI. Cite this article: Bone Joint Res 2021;10(2):96–104.
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Affiliation(s)
- Xinyu Fang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Lvheng Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yuanqing Cai
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Chaofan Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jianhua Lin
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Peter Wahl
- Division of Orthopaedics and Traumatology, Cantonal Hospital Winterthur, Winterthur, Switzerland
| | - Wenming Zhang
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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48
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Esteban J, Gómez-Barrena E. An update about molecular biology techniques to detect orthopaedic implant-related infections. EFORT Open Rev 2021; 6:93-100. [PMID: 33828851 PMCID: PMC8022009 DOI: 10.1302/2058-5241.6.200118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Despite different criteria to diagnose a prosthetic joint infection (PJI), aetiological diagnosis of the causing microorganism remains essential to guide treatment.Molecular-biology-based PJI diagnosis is progressing (faster, higher specificity) in different techniques, from the experimental laboratory into clinical use.Multiplex polymerase chain reaction techniques (custom-made or commercial) provide satisfactory results in clinical series of cases, with specificity close to 100% and sensitivity over 70-80%.Next-generation metagenomics may increase sensitivity while maintaining high specificity.Molecular biology techniques may represent, in the next five years, a significant transformation of the currently available microbiological diagnosis in PJI. Cite this article: EFORT Open Rev 2021;6:93-100. DOI: 10.1302/2058-5241.6.200118.
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Affiliation(s)
- Jaime Esteban
- Servicio de Microbiología Clínica, Hospital Universitario Fundación Jiménez Díaz-IIS-Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Enrique Gómez-Barrena
- Servicio de Cirugía Ortopédica y Traumatología, Hospital Universitario La Paz-IdiPaz, Universidad Autónoma de Madrid, Madrid, Spain
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49
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Fang X, Cai Y, Mei J, Huang Z, Zhang C, Yang B, Li W, Zhang W. Optimizing culture methods according to preoperative mNGS results can improve joint infection diagnosis. Bone Joint J 2021; 103-B:39-45. [PMID: 33380187 DOI: 10.1302/0301-620x.103b1.bjj-2020-0771.r2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AIMS Metagenomic next-generation sequencing (mNGS) is useful in the diagnosis of infectious disease. However, while it is highly sensitive at identifying bacteria, it does not provide information on the sensitivity of the organisms to antibiotics. The purpose of this study was to determine whether the results of mNGS can be used to guide optimization of culture methods to improve the sensitivity of culture from intraoperative samples. METHODS Between July 2014 and October 2019, patients with suspected joint infection (JI) from whom synovial fluid (SF) was obtained preoperatively were enrolled. Preoperative aspirated SF was analyzed by conventional microbial culture and mNGS. In addition to samples taken for conventional microbial culture, some samples were taken for intraoperative culture to optimize the culture method according to the preoperative mNGS results. The demographic characteristics, medical history, laboratory examination, mNGS, and culture results of the patients were recorded, and the possibility of the optimized culture methods improving diagnostic efficiency was evaluated. RESULTS A total of 56 cases were included in this study. There were 35 cases of JI and 21 cases of non-joint infection (NJI). The sensitivity, specificity, and accuracy of intraoperative microbial culture after optimization of the culture method were 94.29%, 76.19%, and 87.5%, respectively, while those of the conventional microbial culture method were 60%, 80.95%, and 67.86%, respectively. CONCLUSION Preoperative aspirated SF detected via mNGS can provide more aetiological information than preoperative culture, which can guide the optimization and improve the sensitivity of intraoperative culture. Cite this article: Bone Joint J 2021;103-B(1):39-45.
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Affiliation(s)
- Xinyu Fang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yuanqing Cai
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jian Mei
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Chaofan Zhang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Bin Yang
- Department of Laboratory Medicine, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopedic Surgery, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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50
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Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
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Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
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