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Fida M, Tande AJ. State-of-the-Art Metagenomic Sequencing and Its Role in the Diagnosis of Periprosthetic Joint Infections. Infect Dis Clin North Am 2024:S0891-5520(24)00062-X. [PMID: 39277504 DOI: 10.1016/j.idc.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2024]
Abstract
Metagenomic next-generation sequencing (mNGS) is increasingly being recognized as a valuable diagnostic tool for periprosthetic joint infections (PJIs). This study reviews the diagnostic utility of mNGS, highlighting its improved sensitivity in detecting pathogens, particularly in culture-negative and polymicrobial infections. However, the clinical application of this method is hindered by challenges such as the prevalence of host DNA, the necessity for extensive bioinformatic analysis, and the potential for contamination, which can lead to misinterpretation of results. As mNGS continues to evolve, it holds significant potential to improve the management of PJI and enhance the application of precision medicine in orthopedic infections.
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Affiliation(s)
- Madiha Fida
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Aaron J Tande
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN, USA
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2
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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; 32:2277-2289. [PMID: 38713871 DOI: 10.1002/ksa.12227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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Yoon JG, Lim S, Hyun HJ, Seong H, Noh JY, Song JY, Kim WJ, Cheong HJ. Respiratory microbiome and clinical course of carbapenem-resistant Acinetobacter baumannii pneumonia in critically Ill patients. Medicine (Baltimore) 2024; 103:e38988. [PMID: 39093794 PMCID: PMC11296444 DOI: 10.1097/md.0000000000038988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) pneumonia has been a serious problem in the intensive care unit (ICU). However, defined characteristics of respiratory microbiome in CRAB pneumonia are lacking nowadays. This study aimed to analyze respiratory microbiome of CRAB pneumonia compared to non-CRAB pneumonia and reveal the clinical significance of respiratory microbiome data in these patients. Patients diagnosed with severe pneumonia with mechanical ventilation were enrolled in the ICU of a tertiary care hospital. Respiratory specimens were collected on days 1, 4, 7, and 14 in each participant via tracheal aspiration. Clinical data and outcomes of each enrolled patient were collected via electronic medical records. Microbiome analysis was conducted with collected respiratory specimens undergone by next-generation sequencing of microbial 16S ribosomal DNA. Six CRAB pneumonia, 4 non-CRAB pneumonia and 5 healthy controls were enrolled. In CRAB pneumonia, CRAB was detected in 3 patients by sputum culture at day 1, while it was negative at day 1 and detected later in the others by follow-up sputum culture. Beta diversity plot analysis showed differences between each group. Shannon index was decreased markedly at day 4 in CRAB pneumonia compared to the others. Among CRAB pneumonia cases, 3 respiratory specimens were culture-negative, but positive by microbiome analysis. Lower respiratory microbiome in CRAB pneumonia had distinct characteristics and early loss of diversity compared to non-CRAB pneumonia, which might be related to poor clinical course. Moreover, CRAB acquisition and colonization would be predicted by preemptive microbiome analysis, which will contribute to effective infection control in the ICU.
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Affiliation(s)
- Jin Gu Yoon
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sooyeon Lim
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center-KU Medicine, Seoul, Republic of Korea
| | - Hak-Jun Hyun
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hye Seong
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ji Yun Noh
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center-KU Medicine, Seoul, Republic of Korea
| | - Joon Young Song
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center-KU Medicine, Seoul, Republic of Korea
| | - Woo Joo Kim
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center-KU Medicine, Seoul, Republic of Korea
| | - Hee Jin Cheong
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
- Asia Pacific Influenza Institute, Korea University College of Medicine, Seoul, Republic of Korea
- Vaccine Innovation Center-KU Medicine, Seoul, Republic of Korea
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Rao PS, Downie DL, David-Ferdon C, Beekmann SE, Santibanez S, Polgreen PM, Kuehnert M, Courtney S, Lee JS, Chaitram J, Salerno RM, Gundlapalli AV. Pathogen-Agnostic Advanced Molecular Diagnostic Testing for Difficult-to-Diagnose Clinical Syndromes-Results of an Emerging Infections Network Survey of Frontline US Infectious Disease Clinicians, May 2023. Open Forum Infect Dis 2024; 11:ofae395. [PMID: 39113826 PMCID: PMC11304606 DOI: 10.1093/ofid/ofae395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024] Open
Abstract
During routine clinical practice, infectious disease physicians encounter patients with difficult-to-diagnose clinical syndromes and may order advanced molecular testing to detect pathogens. These tests may identify potential infectious causes for illness and allow clinicians to adapt treatments or stop unnecessary antimicrobials. Cases of pathogen-agnostic disease testing also provide an important window into known, emerging, and reemerging pathogens and may be leveraged as part of national sentinel surveillance. A survey of Emerging Infections Network members, a group of infectious disease providers in North America, was conducted in May 2023. The objective of the survey was to gain insight into how and when infectious disease physicians use advanced molecular testing for patients with difficult-to-diagnose infectious diseases, as well as to explore the usefulness of advanced molecular testing and barriers to use. Overall, 643 providers answered at least some of the survey questions; 478 (74%) of those who completed the survey had ordered advanced molecular testing in the last two years, and formed the basis for this study. Respondents indicated that they most often ordered broad-range 16S rRNA gene sequencing, followed by metagenomic next-generation sequencing and whole genome sequencing; and commented that in clinical practice, some, but not all tests were useful. Many physicians also noted several barriers to use, including a lack of national guidelines and cost, while others commented that whole genome sequencing had potential for use in outbreak surveillance. Improving frontline physician access, availability, affordability, and developing clear national guidelines for interpretation and use of advanced molecular testing could potentially support clinical practice and public health surveillance.
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Affiliation(s)
- Preetika S Rao
- Office of Public Health Data, Surveillance and Technology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Diane L Downie
- Office of Readiness and Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Corinne David-Ferdon
- National Center for Injury Prevention and Control, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Susan E Beekmann
- Emerging Infections Network, University of Iowa, Iowa City, Iowa, USA
| | - Scott Santibanez
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Philip M Polgreen
- Emerging Infections Network, University of Iowa, Iowa City, Iowa, USA
| | - Matthew Kuehnert
- National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sean Courtney
- Office of Laboratory Systems and Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Justin S Lee
- Global Health Center, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jasmine Chaitram
- Office of Laboratory Systems and Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Reynolds M Salerno
- Office of Laboratory Systems and Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Adi V Gundlapalli
- Office of Public Health Data, Surveillance and Technology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Tarabichi S, Johnson RM, Quinlan ND, Dennis DA, Parvizi J, Jennings JM. Commercial Synovial Antigen Testing is Inferior to Traditional Culture for the Diagnosis of Periprosthetic Joint Infection in Patients Undergoing Revision Total Knee Arthroplasty. J Arthroplasty 2024; 39:S300-S304.e2. [PMID: 38599530 DOI: 10.1016/j.arth.2024.03.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Despite its limitations, a culture remains the "gold standard" for pathogen identification in patients who have periprosthetic joint infection (PJI). Recently, a synovial fluid antigen test has been introduced by a commercial entity. The purpose of this multicenter study was to determine the accuracy of the antigen test in the diagnosis of PJI. METHODS This retrospective study identified 613 patients undergoing revision total knee arthroplasty who had undergone preoperative synovial fluid analysis. A PJI was defined using the 2018 International Consensus Meeting (ICM) criteria. Patients who had an extended period (> 180 days) from aspiration to revision procedure (n = 62), those presenting within 90 days of their index arthroplasty procedure (n = 17), and patients who had an inconclusive ICM score (n = 8) were excluded. Using receiver operator characteristic curve analyses, we examined the utility of the microbial identification (MID) antigen test and any positive culture (either preoperative or intraoperative) in the diagnosis of PJI. RESULTS A total of 526 patients were included. Of these, 125 (23.8%) were ICM positive and 401 (76.2%) were ICM negative. Culture demonstrated an area under the curve (AUC) of 0.864, sensitivity of 75.2%, and specificity of 97.5%. On the other hand, the MID test exhibited an AUC of 0.802, sensitivity of 61.6%, and specificity of 98.8%. The AUC of culture was significantly higher than that of the MID test (P = .037). The MID test was positive in 41.9% of culture-negative PJI cases. We also observed a high rate of discordance (29.7%) when both culture and the MID test were positive in the ICM-positive group. CONCLUSIONS Synovial fluid antigen testing does not provide additional clinical benefit when compared to traditional cultures for the diagnosis of PJI. The antigen test had low sensitivity in the diagnosis of PJI and a relatively high rate of discordance with culture. LEVEL OF EVIDENCE Level III.
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Affiliation(s)
- Saad Tarabichi
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Roseann M Johnson
- Colorado Joint Replacement, Orthopedic Sugery, AdventHealth Porter, Denver, Colorado
| | - Nicole D Quinlan
- Colorado Joint Replacement, Orthopedic Sugery, AdventHealth Porter, Denver, Colorado
| | - Douglas A Dennis
- Colorado Joint Replacement, Orthopedic Sugery, AdventHealth Porter, Denver, Colorado
| | - Javad Parvizi
- International Joint Center, Acibadem University Hospital, Istanbul, Turkey
| | - Jason M Jennings
- Colorado Joint Replacement, Orthopedic Sugery, AdventHealth Porter, Denver, Colorado
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Giarritiello F, Romanò CL, Lob G, Benevenia J, Tsuchiya H, Zappia E, Drago L. Enhancing Pathogen Detection in Implant-Related Infections through Chemical Antibiofilm Strategies: A Comprehensive Review. Antibiotics (Basel) 2024; 13:678. [PMID: 39061360 PMCID: PMC11274042 DOI: 10.3390/antibiotics13070678] [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: 06/27/2024] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Implant-related infections (IRIs) represent a significant challenge to modern surgery. The occurrence of these infections is due to the ability of pathogens to aggregate and form biofilms, which presents a challenge to both the diagnosis and subsequent treatment of the infection. Biofilms provide pathogens with protection from the host immune response and antibiotics, making detection difficult and complicating both single-stage and two-stage revision procedures. This narrative review examines advanced chemical antibiofilm techniques with the aim of improving the detection and identification of pathogens in IRIs. The articles included in this review were selected from databases such as PubMed, Scopus, MDPI and SpringerLink, which focus on recent studies evaluating the efficacy and enhanced accuracy of microbiological sampling and culture following the use of chemical antibiofilm. Although promising results have been achieved with the successful application of some antibiofilm chemical pre-treatment methods, mainly in orthopedics and in cardiovascular surgery, further research is required to optimize and expand their routine use in the clinical setting. This is necessary to ensure their safety, efficacy and integration into diagnostic protocols. Future studies should focus on standardizing these techniques and evaluating their effectiveness in large-scale clinical trials. This review emphasizes the importance of interdisciplinary collaboration in developing reliable diagnostic tools and highlights the need for innovative approaches to improve outcomes for patients undergoing both single-stage and two-stage revision surgery for implant-related infections.
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Affiliation(s)
- Fabiana Giarritiello
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy; (F.G.); (E.Z.)
| | | | - Guenter Lob
- Section Injury Prevention, Deutsche Gesellschaft für Orthopädie und Unfallchirurgie (DGOU), 10117 Berlin, Germany;
| | - Joseph Benevenia
- Orthopaedics Department, Rutgers New Jersey Medical School, Newark, NJ 07103, USA;
| | - Hiroyuki Tsuchiya
- Department of Orthopaedic Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa 921-8641, Japan;
| | - Emanuele Zappia
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy; (F.G.); (E.Z.)
| | - Lorenzo Drago
- Clinical Microbiology and Microbiome Laboratory, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
- UOC Laboratory of Clinical Medicine with Specialized Areas, IRCCS MultiMedica, 20138 Milan, Italy
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Thompson E, Qureshi A. Pathogens in FRI - Do bugs matter? - An analysis of FRI studies to assess your enemy. J Orthop 2024; 53:59-72. [PMID: 38476676 PMCID: PMC10925936 DOI: 10.1016/j.jor.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Fracture-related infection (FRI) is a devasting complication for both patients and their treating Orthopaedic surgeon that can lead to loss of limb function or even amputation. The unique and unpredictable features of FRI make its diagnosis and treatment a significant challenge. It has substantial morbidity and financial implications for patients, their families and healthcare providers. In this article, we perform an in-depth and comprehensive review of FRI through recent and seminal literature to highlight evolving definitions, diagnostic and treatment approaches, focusing on common pathogens such as Staphylococcus aureus, polymicrobial infections and multi-drug-resistant organisms (MDRO). Furthermore, multiple resistance mechanisms and adaptations for microbial survival are discussed, as well as modern evidence-based medical and surgical advancements in treatment strategies in combating FRI.
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Affiliation(s)
- Emmet Thompson
- Limb Reconstruction Service, Trauma & Orthopaedic Department, University Hospital Southampton, Southampton, UK
| | - Amir Qureshi
- Limb Reconstruction Service, Trauma & Orthopaedic Department, University Hospital Southampton, Southampton, UK
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Azad MA, Patel R. Practical Guidance for Clinical Microbiology Laboratories: Microbiologic diagnosis of implant-associated infections. Clin Microbiol Rev 2024; 37:e0010423. [PMID: 38506553 PMCID: PMC11237642 DOI: 10.1128/cmr.00104-23] [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] [Indexed: 03/21/2024] Open
Abstract
SUMMARYImplant-associated infections (IAIs) pose serious threats to patients and can be associated with significant morbidity and mortality. These infections may be difficult to diagnose due, in part, to biofilm formation on device surfaces, and because even when microbes are found, their clinical significance may be unclear. Despite recent advances in laboratory testing, IAIs remain a diagnostic challenge. From a therapeutic standpoint, many IAIs currently require device removal and prolonged courses of antimicrobial therapy to effect a cure. Therefore, making an accurate diagnosis, defining both the presence of infection and the involved microorganisms, is paramount. The sensitivity of standard microbial culture for IAI diagnosis varies depending on the type of IAI, the specimen analyzed, and the culture technique(s) used. Although IAI-specific culture-based diagnostics have been described, the challenge of culture-negative IAIs remains. Given this, molecular assays, including both nucleic acid amplification tests and next-generation sequencing-based assays, have been used. In this review, an overview of these challenging infections is presented, as well as an approach to their diagnosis from a microbiologic perspective.
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Affiliation(s)
- Marisa Ann Azad
- Division of Infectious Diseases, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canada
| | - Robin Patel
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Tsai SW, Mu W, Parvizi J. Culture-negative periprosthetic joint infections: Do we have an issue? J Clin Orthop Trauma 2024; 52:102430. [PMID: 38783996 PMCID: PMC11108966 DOI: 10.1016/j.jcot.2024.102430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Culture-negative periprosthetic joint infection (PJI) poses a significant challenge in clinical settings. The lack of information on causative organism(s) leads to uncertainties regarding the choice of antimicrobial treatment, which can potentially adversely influence the outcome. Recent advances in molecular-based diagnostic methods have the potential to address the difficulties associated with culture-negative PJIs. These technologies offer a solution to the existing clinical dilemma by providing identification of pathogens and guiding appropriate antimicrobial treatment. In this narrative review, we provide information regarding: 1) incidence and risk factors for culture-negative PJI; 2) the optimal antimicrobial therapy and duration of treatment for culture-negative PJI; 3) outcome comparison between culture-positive and culture-negative PJI; and 4) utilization of novel molecular diagnostic methods in culture-negative PJI, including pathogen identification, and the implementation of an antibiotic stewardship program.
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Affiliation(s)
- Shang-Wen Tsai
- Department of Orthopaedics and Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Orthopaedics, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA, USA
| | - Wenbo Mu
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA, USA
- Department of Orthopaedics, First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Javad Parvizi
- International Joint Center, Acibadem University, Istanbul, Turkey
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10
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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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11
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Li C, Xiao NS, Ke BY, Li S, Lin Y. Application of Metagenomic Next-Generation Sequencing in Suspected Spinal Infectious Diseases. World Neurosurg 2024; 185:e542-e548. [PMID: 38401756 DOI: 10.1016/j.wneu.2024.02.071] [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: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/26/2024]
Abstract
OBJECTIVE This study aimed to explore the clinical efficacy of metagenomic next-generation sequencing (mNGS) in diagnosing and treating suspected spinal infectious diseases. METHODS Between October 2022 to December 2023, a retrospective analysis was performed on patient records within the Department of Spinal Surgery at Guilin People's Hospital. The analysis included comprehensive data on patients with presumed spinal infectious diseases, incorporating results from mNGS tests conducted externally, conventional pathogen detection results, laboratory examination results, and imaging findings. The study aimed to assess the applicability of mNGS in the context of suspected spinal infectious lesions. RESULTS Twenty-seven patients were included in the final analysis. Pathogenic microorganisms were identified in 23 cases. The included cases encompassed 1 case of tuberculous spondylitis, 1 case of fungal infection, 3 cases of Brucella spondylitis, 3 cases of viral infection, 9 cases of bacterial infection, and 6 cases of mixed infections. Pathogenic microorganisms remained elusive in 4 cases. The application of the mNGS method demonstrated a significantly elevated positive detection rate compared to conventional methods (85.19% vs. 48.15%, P < 0.05). Moreover, the mNGS method detected a greater variety of pathogen species than traditional methods (Z = 10.69, P < 0.05). Additionally, the mNGS method exhibited a shorter detection time. CONCLUSIONS mNGS demonstrated significantly higher detection rates for bacterial, fungal, viral, and mixed infections in cases of suspected spinal infectious diseases. The clinical implementation of mNGS could further enhance the efficiency of diagnosing and treating suspected spinal infectious diseases.
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Affiliation(s)
- Cheng Li
- Department of Orthopaedics, Guilin People's Hospital, Guilin, Guangxi Province, China
| | - Nian-Su Xiao
- Department of Orthopaedics, Guilin People's Hospital, Guilin, Guangxi Province, China
| | - Bao-Yi Ke
- Department of Orthopaedics, Guilin People's Hospital, Guilin, Guangxi Province, China
| | - Sen Li
- Department of Orthopaedics, Guilin People's Hospital, Guilin, Guangxi Province, China
| | - Yang Lin
- Department of Orthopaedics, Guilin People's Hospital, Guilin, Guangxi Province, China.
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12
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Cai S, Pan J, Wang S, Bao R, Zhou C, Gao X, Shiiya H, Hu B. Accurate etiological diagnosis of Mycoplasma hominis mediastinitis in immunocompetent patients using metagenomic next-generation sequencing: a case series and literature review. J Thorac Dis 2024; 16:2499-2509. [PMID: 38738251 PMCID: PMC11087618 DOI: 10.21037/jtd-24-286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/07/2024] [Indexed: 05/14/2024]
Abstract
Background As a culture-independent method, metagenomic next-generation sequencing (mNGS) is widely used in microbiological diagnosis with advantages in identifying potential pathogens, guiding antibiotic therapy, and improving clinical prognosis, especially in culture-negative cases. Mycoplasma hominis (M. hominis) mediastinitis is a rare and severe disease for which etiological diagnosis is important but challenging. The application of mNGS in the etiological diagnosis of mediastinitis has seldom been studied. Methods By searching the electronic medical history retrieval system with "Mycoplasma hominis" and "mediastinitis", seven patients diagnosed with M. hominis mediastinitis were reviewed in Zhongshan Hospital, Fudan University, Shanghai from 9 December 2020 to 14 February 2023. Microbiological cultures and mNGS were conducted for blood, abscess, and/or mediastinal fluid. Adjustment of the antibiotic therapy due to mNGS was assessed. A literature review was conducted in the PubMed database beginning in 1970 for M. hominis infection and mediastinitis. Results For the seven patients, cultures of blood, abscess, and mediastinal fluid were negative whereas mNGS identified M. hominis in serum, abscess, and/or mediastinal fluid and was used to guide specific antibiotic therapy. The stringent mapped reads number of genera (SMRNG), stringent mapped reads number of species (SMRN), and coverage rate of M. hominis detection by mNGS were significantly higher in body fluid (abscess or mediastinal fluid) than in serum. All seven patients had underlying heart diseases and underwent previous cardiac surgery. The most common symptoms were fever and sternal pain. After detection of M. hominis, antibiotics were adjusted to quinolones or doxycycline except for one patient, whose diagnosis was clarified after death. Two patients died. Literature review since 1970 identified 30 cases of extra-genital infection caused by M. hominis. Including our seven new cases, 2 (5.4%) were neonates and 35 (94.6%) were adults. Thirty (81.1%) cases were postoperative infection and 15 (40.5%) had implanted devices. Five patients (13.5%) died. Conclusions mNGS might be a promising technology in the detection of fastidious pathogens such as M. hominis. Accurate etiological diagnosis by mNGS could guide antibiotic therapy and facilitate clinical management.
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Affiliation(s)
- Sishi Cai
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jue Pan
- Department of Infectious Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Suzhen Wang
- Department of Microbiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rong Bao
- Department of Microbiology, 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
| | - Haruhiko Shiiya
- Department of Thoracic Surgery, Hokkaido University Hospital, Sapporo, Japan
| | - 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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13
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Kufner V, Frey AC, Burkhard SH, Schmutz S, Ziltener G, Zaheri M, Wiedmer CV, Plate A, Trkola A, Huber M, Mueller NJ. Exploring viral aetiology in upper respiratory tract infections: insights from metagenomic next-generation sequencing in Swiss outpatients before and during the SARS-CoV-2 pandemic. Swiss Med Wkly 2024; 154:3797. [PMID: 38587784 DOI: 10.57187/s.3797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
AIMS OF THE STUDY Upper respiratory tract infections are among the most common reasons for primary care consultations. They are diagnosed predominantly based on clinical assessment. Here, we investigated the benefit of viral metagenomic next-generation sequencing (mNGS) in an outpatient setting. METHODS This prospective cross-sectional study included immunocompetent patients with acute upper respiratory tract infections. General practitioners collected pharyngeal swabs and demographic and clinical data. Specimens were analysed using viral mNGS and conventional tests. RESULTS Two hundred seventy-seven patients were recruited by 21 general practitioners between 10/2019 and 12/2020, of which 91% had a suspected viral aetiology. For 138 patients (49.8%), mNGS identified one or more respiratory viruses. The mNGS showed a high overall agreement with conventional routine diagnostic tests. Rhinoviruses were the most frequently detected respiratory viruses (20.2% of patients). Viral mNGS reflected the influenza wave in early 2020 and the SARS-CoV-2 pandemic outbreak in Switzerland in March 2020. Notably, rhinoviruses continued to circulate despite non-pharmaceutical hygiene measures. CONCLUSIONS Viral mNGS allowed the initial diagnosis to be retrospectively re-evaluated. Assuming reduced turnaround times, mNGS has the potential to directly guide the treatment of upper respiratory tract infections. On an epidemiological level, our study highlights the utility of mNGS in respiratory infection surveillance, allowing early detection of epidemics and providing information crucial for prevention.
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Affiliation(s)
- Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Andrea C Frey
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Sara H Burkhard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Gabriela Ziltener
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Caroline V Wiedmer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Andreas Plate
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nicolas J Mueller
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
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14
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Deans CF, Kildow BJ, Garvin KL. Recurrent Periprosthetic Joint Infections: Diagnosis, Management, and Outcomes. Orthop Clin North Am 2024; 55:193-206. [PMID: 38403366 DOI: 10.1016/j.ocl.2023.09.002] [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] [Indexed: 02/27/2024]
Abstract
Periprosthetic joint infection (PJI) remains one of the most common complications after total joint arthroplasty. It is challenging to manage, associated with significant morbidity and mortality, and is a financial burden on the health care system. Failure of 2-stage management for chronic PJI is not uncommon. Repeat infections are oftentimes polymicrobial, multiple drug-resistant microorganisms, or new organisms. Optimizing the success of index 2-stage revision is the greatest prevention against failure of any subsequent management options and requires a robust team-based approach.
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Affiliation(s)
- Christopher F Deans
- Department of Orthopaedic Surgery and Rehabilitation, University of Nebraska Medical Center, 985640 Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Beau J Kildow
- Department of Orthopaedic Surgery and Rehabilitation, University of Nebraska Medical Center, 985640 Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kevin L Garvin
- Department of Orthopaedic Surgery and Rehabilitation, University of Nebraska Medical Center, 985640 Nebraska Medical Center, Omaha, NE 68198, USA
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Ward SA, Habibi AA, Ashkenazi I, Arshi A, Meftah M, Schwarzkopf R. Innovations in the Isolation and Treatment of Biofilms in Periprosthetic Joint Infection: A Comprehensive Review of Current and Emerging Therapies in Bone and Joint Infection Management. Orthop Clin North Am 2024; 55:171-180. [PMID: 38403364 DOI: 10.1016/j.ocl.2023.10.002] [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] [Indexed: 02/27/2024]
Abstract
Periprosthetic joint infections (PJIs) are a devastating complication of joint arthroplasty surgeries that are often complicated by biofilm formation. The development of biofilms makes PJI treatment challenging as they create a barrier against antibiotics and host immune responses. This review article provides an overview of the current understanding of biofilm formation, factors that contribute to their production, and the most common organisms involved in this process. This article focuses on the identification of biofilms, as well as current methodologies and emerging therapies in the management of biofilms in PJI.
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Affiliation(s)
- Spencer A Ward
- NYU Langone Orthopedic Hospital, NYU Langone Health, 301 East 17th Street, Room 1402, New York, NY 10003, USA
| | - Akram A Habibi
- NYU Langone Orthopedic Hospital, NYU Langone Health, 301 East 17th Street, Room 1402, New York, NY 10003, USA
| | - Itay Ashkenazi
- NYU Langone Orthopedic Hospital, NYU Langone Health, 301 East 17th Street, Room 1402, New York, NY 10003, USA
| | - Armin Arshi
- NYU Langone Orthopedic Hospital, NYU Langone Health, 301 East 17th Street, Room 1402, New York, NY 10003, USA
| | - Morteza Meftah
- NYU Langone Orthopedic Hospital, NYU Langone Health, 301 East 17th Street, Room 1402, New York, NY 10003, USA
| | - Ran Schwarzkopf
- NYU Langone Orthopedic Hospital, NYU Langone Health, 301 East 17th Street, Room 1402, New York, NY 10003, USA.
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16
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Zou H, Gao S, Liu X, Liu Y, Xiao Y, Li A, Jiang Y. Combination of metagenomic next-generation sequencing and conventional tests unraveled pathogen profiles in infected patients undergoing allogeneic hematopoietic stem cell transplantation in Jilin Province of China. Front Cell Infect Microbiol 2024; 14:1378112. [PMID: 38567023 PMCID: PMC10985322 DOI: 10.3389/fcimb.2024.1378112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
Background Infection is the main cause of death for patients after allogeneic hematopoietic stem cell transplantation (HSCT). However, pathogen profiles still have not been reported in detail due to their heterogeneity caused by geographic region. Objective To evaluate the performance of metagenomic next-generation sequencing (mNGS) and summarize regional pathogen profiles of infected patients after HSCT. Methods From February 2021 to August 2022, 64 patients, admitted to the Department of Hematology of The First Hospital of Jilin University for HSCT and diagnosed as suspected infections, were retrospectively enrolled. Results A total of 38 patients were diagnosed as having infections, including bloodstream (n =17), pulmonary (n =16), central nervous system (CNS) (n =4), and chest (n =1) infections. Human betaherpesvirus 5 (CMV) was the most common pathogen in both bloodstream (n =10) and pulmonary (n =8) infections, while CNS (n =2) and chest (n =1) infections were mainly caused by Human gammaherpesvirus 4 (EBV). For bloodstream infection, Mycobacterium tuberculosis complex (n =3), Staphylococcus epidermidis (n =1), and Candida tropicalis (n =1) were also diagnosed as causative pathogens. Furthermore, mNGS combined with conventional tests can identify more causative pathogens with high sensitivity of 82.9% (95% CI 70.4-95.3%), and the total coincidence rate can reach up to 76.7% (95% CI 64.1-89.4%). Conclusions Our findings emphasized the importance of mNGS in diagnosing, managing, and ruling out infections, and an era of more rapid, independent, and impartial diagnosis of infections after HSCT can be expected.
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Affiliation(s)
- Hongyan Zou
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Sujun Gao
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Xiaoliang Liu
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Yong Liu
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Yunping Xiao
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Ao Li
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Yanfang Jiang
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
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17
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Davis JS, Dewar D, Manning L. Prosthetic joint infection diagnosis in an age of changing clinical patterns of infection and new technologies. Med J Aust 2024; 220:225-228. [PMID: 38351733 DOI: 10.5694/mja2.52228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/31/2024] [Indexed: 03/18/2024]
Affiliation(s)
- Joshua S Davis
- University of Newcastle, Newcastle, NSW
- Hunter Medical Research Institute, Newcastle, NSW
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18
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Tan J, Wu L, Zhan L, Sheng M, Tang Z, Xu J, Ma H. Optimal selection of specimens for metagenomic next-generation sequencing in diagnosing periprosthetic joint infections. Front Cell Infect Microbiol 2024; 14:1356804. [PMID: 38500507 PMCID: PMC10945027 DOI: 10.3389/fcimb.2024.1356804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Objective This study aimed to assess the diagnostic value of metagenomic next-generation sequencing (mNGS) across synovial fluid, prosthetic sonicate fluid, and periprosthetic tissues among patients with periprosthetic joint infection (PJI), intending to optimize specimen selection for mNGS in these patients. Methods This prospective study involved 61 patients undergoing revision arthroplasty between September 2021 and September 2022 at the First Affiliated Hospital of Zhengzhou University. Among them, 43 cases were diagnosed as PJI, and 18 as aseptic loosening (AL) based on the American Musculoskeletal Infection Society (MSIS) criteria. Preoperative or intraoperative synovial fluid, periprosthetic tissues, and prosthetic sonicate fluid were collected, each divided into two portions for mNGS and culture. Comparative analyses were conducted between the microbiological results and diagnostic efficacy derived from mNGS and culture tests. Furthermore, the variability in mNGS diagnostic efficacy for PJI across different specimen types was assessed. Results The sensitivity and specificity of mNGS diagnosis was 93% and 94.4% for all types of PJI specimens; the sensitivity and specificity of culture diagnosis was 72.1% and 100%, respectively. The diagnostic sensitivity of mNGS was significantly higher than that of culture (X2 = 6.541, P=0.011), with no statistically significant difference in specificity (X2 = 1.029, P=0.310). The sensitivity of the synovial fluid was 83.7% and the specificity was 94.4%; the sensitivity of the prosthetic sonicate fluid was 90.7% and the specificity was 94.4%; and the sensitivity of the periprosthetic tissue was 81.4% and the specificity was 100%. Notably, the mNGS of prosthetic sonicate fluid displayed a superior pathogen detection rate compared to other specimen types. Conclusion mNGS can function as a precise diagnostic tool for identifying pathogens in PJI patients using three types of specimens. Due to its superior ability in pathogen identification, prosthetic sonicate fluid can replace synovial fluid and periprosthetic tissue as the optimal sample choice for mNGS.
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Affiliation(s)
- Jun Tan
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
| | - Lingxiao Wu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lijuan Zhan
- Department of Neurology, People’s Hospital of Zhengzhou, Zhengzhou, Henan, China
| | - Minkui Sheng
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
| | - Zhongxin Tang
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jianzhong Xu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haijun Ma
- Department of Mini-invasive Spinal Surgery, The Third People’s Hospital of Henan Province, Zhengzhou, Henan, China
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19
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Downie DL, Rao P, David-Ferdon C, Courtney S, Lee JS, Kugley S, MacDonald PDM, Barnes K, Fisher S, Andreadis JL, Chaitram J, Mauldin MR, Salerno RM, Schiffer J, Gundlapalli AV. Literature Review of Pathogen Agnostic Molecular Testing of Clinical Specimens From Difficult-to-Diagnose Patients: Implications for Public Health. Health Secur 2024; 22:93-107. [PMID: 38608237 PMCID: PMC11044852 DOI: 10.1089/hs.2023.0100] [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: 05/22/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 04/14/2024] Open
Abstract
To better identify emerging or reemerging pathogens in patients with difficult-to-diagnose infections, it is important to improve access to advanced molecular testing methods. This is particularly relevant for cases where conventional microbiologic testing has been unable to detect the pathogen and the patient's specimens test negative. To assess the availability and utility of such testing for human clinical specimens, a literature review of published biomedical literature was conducted. From a corpus of more than 4,000 articles, a set of 34 reports was reviewed in detail for data on where the testing was being performed, types of clinical specimens tested, pathogen agnostic techniques and methods used, and results in terms of potential pathogens identified. This review assessed the frequency of advanced molecular testing, such as metagenomic next generation sequencing that has been applied to clinical specimens for supporting clinicians in caring for difficult-to-diagnose patients. Specimen types tested were from cerebrospinal fluid, respiratory secretions, and other body tissues and fluids. Publications included case reports and series, and there were several that involved clinical trials, surveillance studies, research programs, or outbreak situations. Testing identified both known human pathogens (sometimes in new sites) and previously unknown human pathogens. During this review, there were no apparent coordinated efforts identified to develop regional or national reports on emerging or reemerging pathogens. Therefore, development of a coordinated sentinel surveillance system that applies advanced molecular methods to clinical specimens which are negative by conventional microbiological diagnostic testing would provide a foundation for systematic characterization of emerging and underdiagnosed pathogens and contribute to national biodefense strategy goals.
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Affiliation(s)
- Diane L. Downie
- Diane L. Downie, PhD, MPH, is Deputy Associate Director for Science, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Preetika Rao
- Preetika Rao, MPH, is a Health Scientist; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Corinne David-Ferdon
- Corinne David-Ferdon, PhD, is Associate Director of Science, Office of Public Health Data, Surveillance, and Technology; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Sean Courtney
- Sean Courtney, PhD, is a Health Scientist, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Justin S. Lee
- Justin Lee, DVM, PhD, is a Health Scientist, Division of Global Health Protection; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Shannon Kugley
- Shannon Kugley, MLIS, is a Research Public Health Analyst; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Pia D. M. MacDonald
- Pia D. M. MacDonald, PhD, MPH, is a Senior Infectious Disease Epidemiologist; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Keegan Barnes
- Keegan Barnes is a Public Health Analyst; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Shelby Fisher
- Shelby Fisher, MPH, is an Epidemiologist; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Joanne L. Andreadis
- Joanne L. Andreadis, PhD, is Associate Director for Science, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jasmine Chaitram
- Jasmine Chaitram, MPH, is Branch Chief, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Matthew R. Mauldin
- Matthew R. Mauldin, PhD, is Health Scientists, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Reynolds M. Salerno
- Reynolds M. Salerno, PhD, is Director, Division of Laboratory Systems; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jarad Schiffer
- Jarad Schiffer, MS, is Health Scientists, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Adi V. Gundlapalli
- Adi V. Gundlapalli, MD, PhD, is a Senior Advisor, Data Readiness and Response, Office of Public Health Data, Surveillance, and Technology; at the US Centers for Disease Control and Prevention, Atlanta, GA
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20
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Downie DL, Rao P, David-Ferdon C, Courtney S, Lee JS, Quiner C, MacDonald PDM, Barnes K, Fisher S, Andreadis JL, Chaitram J, Mauldin MR, Salerno RM, Schiffer J, Gundlapalli AV. Surveillance for Emerging and Reemerging Pathogens Using Pathogen Agnostic Metagenomic Sequencing in the United States: A Critical Role for Federal Government Agencies. Health Secur 2024; 22:85-92. [PMID: 38574329 PMCID: PMC11044857 DOI: 10.1089/hs.2023.0099] [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: 05/22/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 04/06/2024] Open
Abstract
The surveillance and identification of emerging, reemerging, and unknown infectious disease pathogens is essential to national public health preparedness and relies on fluidity, coordination, and interconnectivity between public and private pathogen surveillance systems and networks. Developing a national sentinel surveillance network with existing resources and infrastructure could increase efficiency, accelerate the identification of emerging public health threats, and support coordinated intervention strategies that reduce morbidity and mortality. However, implementing and sustaining programs to detect emerging and reemerging pathogens in humans using advanced molecular methods, such as metagenomic sequencing, requires making large investments in testing equipment and developing networks of clinicians, laboratory scientists, and bioinformaticians. In this study, we sought to gain an understanding of how federal government agencies currently support such pathogen agnostic testing of human specimens in the United States. We conducted a landscape analysis of federal agency websites for publicly accessible information on the availability and type of pathogen agnostic testing and details on flow of clinical specimens and data. The website analysis was supplemented by an expert review of results with representatives from the federal agencies. Operating divisions within the US Department of Health and Human Services and the US Department of Veterans Affairs have developed and sustained extensive clinical and research networks to obtain patient specimens and perform metagenomic sequencing. Metagenomic facilities supported by US agencies were not equally geographically distributed across the United States. Although many entities have work dedicated to metagenomics and/or support emerging infectious disease surveillance specimen collection, there was minimal formal collaboration across agencies.
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Affiliation(s)
- Diane L. Downie
- Diane L. Downie, PhD, MPH, is Deputy Associate Director for Science, Office of Readiness and Response, US Centers for Disease Control and Prevention, Atlanta, GA
| | - Preetika Rao
- Preetika Rao, MPH, is a Health Scientist, US Centers for Disease Control and Prevention, Atlanta, GA
| | - Corinne David-Ferdon
- Corinne David-Ferdon, PhD, is Associate Director of Science, Office of Public Health Data, Surveillance, and Technology, US Centers for Disease Control and Prevention, Atlanta, GA
| | - Sean Courtney
- Sean Courtney, PhD, is a Health Scientist, US Centers for Disease Control and Prevention, Atlanta, GA
| | - Justin S. Lee
- Justin S. Lee, DVM, PhD, is a Health Scientist, Division of Global Health Protection, US Centers for Disease Control and Prevention, Atlanta, GA
| | - Claire Quiner
- Claire Quiner, MPH, MCP, is a Research Public Health Analyst, Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Pia D. M. MacDonald
- Pia D. M. MacDonald, PhD, MPH, is a Senior Infectious Disease Epidemiologist, Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Keegan Barnes
- Keegan Barnes is a Public Health Analyst, Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Shelby Fisher
- Shelby Fisher, MPH, is an Epidemiologist, Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Joanne L. Andreadis
- Joanne L. Andreadis, PhD, is Associate Director for Science, US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jasmine Chaitram
- Jasmine Chaitram, MPH, is Branch Chief, US Centers for Disease Control and Prevention, Atlanta, GA
| | - Matthew R. Mauldin
- Matthew R. Mauldin, PhD, is Health Scientists US Centers for Disease Control and Prevention, Atlanta, GA
| | - Reynolds M. Salerno
- Reynolds M. Salerno, PhD, is Director, Division of Laboratory Systems, US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jarad Schiffer
- Jarad Schiffer, MS, is Health Scientists, Office of Readiness and Response, US Centers for Disease Control and Prevention, Atlanta, GA
| | - Adi V. Gundlapalli
- Adi V. Gundlapalli, MD, PhD, is a Senior Advisor, Data Readiness and Response, Office of Public Health Data, Surveillance, and Technology, US Centers for Disease Control and Prevention, Atlanta, GA
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21
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Yang S, Kozyreva VK, Timme RE, Hemarajata P. Editorial: Integration of NGS in clinical and public health microbiology workflows: applications, compliance, quality considerations. Front Public Health 2024; 12:1357098. [PMID: 38322128 PMCID: PMC10845330 DOI: 10.3389/fpubh.2024.1357098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/15/2024] [Indexed: 02/08/2024] Open
Affiliation(s)
- Shangxin Yang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Varvara K. Kozyreva
- Microbial Diseases Laboratory, California Department of Public Health, Richmond, CA, United States
| | - Ruth E. Timme
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, MD, United States
| | - Peera Hemarajata
- Association of Public Health Laboratories, Silver Spring, MD, United States
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22
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Qian Z, Xia H, Zhou J, Wang R, Zhu D, Chen L, Kang H, Feng J, Hu X, Wang L, Xu S, Lou Z, Tao Y. Performance of Metagenomic Next-Generation Sequencing of Cell-Free DNA From Vitreous and Aqueous Humor for Diagnoses of Intraocular Infections. J Infect Dis 2024; 229:252-261. [PMID: 37882788 DOI: 10.1093/infdis/jiad363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/28/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Delayed diagnosis and improper therapy for intraocular infections usually result in poor prognosis. Due to limitations of conventional culture and polymerase chain reaction methods, most causative pathogens cannot be identified from vitreous humor (VH) or aqueous humor (AH) samples with limited volume. METHODS Patients with suspected intraocular infections were enrolled from January 2019 to August 2021. Metagenomic next-generation sequencing (mNGS) was used to detected causative pathogens. RESULTS This multicenter prospective study enrolled 488 patients, from whom VH (152) and AH (336) samples were respectively collected and analyzed using mNGS of cell-free DNA (cfDNA). Taking final comprehensive clinical diagnosis as the gold standard, there were 39 patients with indefinite final diagnoses, whereas 288 and 161 patients were diagnosed as definite infectious and noninfectious diseases, respectively. Based on clinical adjudication, the sensitivity (92.2%) and total coincidence rate (81.3%) of mNGS using VH samples were slightly higher than those of mNGS using AH samples (85.4% and 75.4%, respectively). CONCLUSIONS Using mNGS of cfDNA, an era with clinical experience for more rapid, independent, and impartial diagnosis of bacterial and other intraocular infections can be expected.
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Affiliation(s)
- Zhuyun Qian
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
- Key Laboratory jointly built by the National Institute for Viral Disease Control and Prevention of China Center for Disease Control and Prevention, Beijing GIANTMED Medical Diagnostics Laboratory
- Department of Medicine, Beijing GIANTMED Medical Diagnostics Laboratory
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co, Ltd, Beijing
| | - Jiemin Zhou
- Department of Scientific Affairs, Hugobiotech Co, Ltd, Beijing
| | - Ruifeng Wang
- Department of Ophthalmology, Zhengzhou Second People's Hospital, Zhengzhou, Henan
| | - Dan Zhu
- Department of Ophthalmology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia
| | - Li Chen
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
| | - Hao Kang
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
| | - Jing Feng
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
| | - Xiaofeng Hu
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
| | - Lu Wang
- Department of Medicine, Beijing GIANTMED Medical Diagnostics Laboratory
| | - Songtao Xu
- National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, China
| | - Zheng Lou
- Department of Scientific Affairs, Hugobiotech Co, Ltd, Beijing
| | - Yong Tao
- Department of Ophthalmology, Beijing Chaoyang Hospital, Capital Medical University
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Hao L, Bian W, Qing Z, Ma T, Li H, Xu P, Wen P. Will previous antimicrobial therapy reduce the positivity rate of metagenomic next-generation sequencing in periprosthetic joint infections? A clinical study. Front Cell Infect Microbiol 2024; 13:1295962. [PMID: 38274732 PMCID: PMC10808557 DOI: 10.3389/fcimb.2023.1295962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a culture-independent massively parallel DNA sequencing technology and it has been widely used for rapid etiological diagnosis with significantly high positivity rate. Currently, clinical studies on evaluating the influence of previous antimicrobial therapy on positivity rate of mNGS in PJIs are rarely reported. The present study aimed to investigate whether the positivity rate of mNGS is susceptible to previous antimicrobial therapy. Methods We performed a prospective trial among patients who undergone hip or knee surgery due to periprosthetic joint infection (PJI) to compare the positivity rate of culture and mNGS between cases with and without previous antimicrobial therapy, and the positivity rates between cases with different antimicrobial-free intervals were also analysed. Results Among 131 included PJIs, 91 (69.5%) had positive cultures and 115 (87.8%) had positive mNGS results. There was no significant difference in the positivity rate of deep-tissue culture and synovial fluid mNGS between cases with and without previous antimicrobial therapy. The positivity rate of synovial fluid culture was higher in cases with previous antimicrobial therapy. The positivity rates of mNGS in synovial fluid decreased as the antimicrobial-free interval ranged from 4 to 14 days to 0 to 3 days. Conclusion mNGS is more advantageous than culture with a higher pathogen detection rate. However, our data suggested that antimicrobial agents may need to be discontinued more than 3 days before sampling to further increase the positivity rate of mNGS for PJIs.
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Affiliation(s)
- Linjie Hao
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
- Department of Orthopedics, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Weiguo Bian
- Department of Orthopedics, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Zhong Qing
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Tao Ma
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Hui Li
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Peng Xu
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Pengfei Wen
- Department of Joint Surgery, Honghui Hospital, Xi’an Jiaotong University, Xi’an, China
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Lin W, Xie F, Li X, Yang R, Lu J, Ruan Z, Ou D, Wang Z. Diagnostic performance of metagenomic next-generation sequencing and conventional microbial culture for spinal infection: a retrospective comparative study. EUROPEAN SPINE JOURNAL : OFFICIAL PUBLICATION OF THE EUROPEAN SPINE SOCIETY, THE EUROPEAN SPINAL DEFORMITY SOCIETY, AND THE EUROPEAN SECTION OF THE CERVICAL SPINE RESEARCH SOCIETY 2023; 32:4238-4245. [PMID: 37689612 DOI: 10.1007/s00586-023-07928-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 07/26/2023] [Accepted: 08/28/2023] [Indexed: 09/11/2023]
Abstract
PURPOSE The study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) as a diagnostic test for biopsy samples from patients with suspected spinal infection (SI) and compared the diagnostic performance of mNGS with that of microbial culture. METHODS All patients diagnosed with clinical suspicion of SI were enrolled, and data were collected through a retrospective chart review of patient records. Biopsy specimens obtained from each patient were tested via mNGS and microbial culture. Samples were enriched for microbial DNA using the universal DNA extraction kit, whole-genome amplified, and sequenced using MGISEQ-200 instrument. After Low-quality reads removed, the remaining sequences for microbial content were analyzed and aligned using SNAP and kraken2 tools. RESULTS A total of 39 patients (19 men and 20 women) were deemed suitable for enrollment. The detection rate for pathogens of mNGS was 71.8% (28/39), which was significantly higher than that of microbial culture (23.1%, p = 0.016). Mycobacterium tuberculosis complex was the most frequently isolated. Using pathologic test as the standard reference for SI, thirty-one cases were classified as infected, and eight cases were considered aseptic. The sensitivity and specificity values for detecting pathogens with mNGS were 87.1% and 87.5%, while these rates were 25.8% and 87.5% with conventional culture. mNGS was able to detect 88.9% (8/9) of pathogens identified by conventional culture, with a genus-level sensitivity of 100% (8/8) and a species-level sensitivity of 87.5% (7/8). CONCLUSION The present work suggests that mNGS might be superior to microbial culture for detecting SI pathogens.
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Affiliation(s)
- Wentao Lin
- Department of Spine Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), No. 1 Jiazi Rd, Shunde District, Foshan City, Guangdong Province, China
| | - Faqin Xie
- Department of Spine Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), No. 1 Jiazi Rd, Shunde District, Foshan City, Guangdong Province, China
| | - Xinan Li
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ruobing Yang
- Department of Spine Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), No. 1 Jiazi Rd, Shunde District, Foshan City, Guangdong Province, China
| | - Junan Lu
- Department of Spine Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), No. 1 Jiazi Rd, Shunde District, Foshan City, Guangdong Province, China
| | - Zheng Ruan
- Department of Spine Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), No. 1 Jiazi Rd, Shunde District, Foshan City, Guangdong Province, China
| | - Dingqiang Ou
- Department of Spine Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), No. 1 Jiazi Rd, Shunde District, Foshan City, Guangdong Province, China
| | - Zhiyun Wang
- Department of Spine Surgery, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), No. 1 Jiazi Rd, Shunde District, Foshan City, Guangdong Province, China.
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Kimseng H, Rossi G, Danjean M, Jimenez-Araya B, Chaligne C, Galy A, Souhail B, Bert F, Leflon V, Fihman V, Caillault A, Demontant V, Seng S, Trawinski E, N 'Debi M, Boizeau L, Jacquier H, Ronot M, Reizine E, Le Roy V, Lefort A, Rodriguez C, Lepeule R, Woerther PL. Evaluation of the contribution of shotgun metagenomics in the microbiological diagnosis of liver abscesses. J Infect 2023; 87:365-372. [PMID: 37604210 DOI: 10.1016/j.jinf.2023.08.004] [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: 07/07/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Shotgun metagenomics (SMg) sequencing has gained a considerable interest, as it enables the detection of any microorganisms through a single analysis. Due to the limitations of standard microbiological approaches, the microbial documentation of liver abscesses (LA), which is crucial for their medical management, can be difficult. Here we aimed to compare the performance of SMg with standard approaches for the microbiological documentation of LA. METHODS In this retrospective study conducted at two centers, we compared the results of standard microbiology with metagenomics analysis of consecutive LA samples. For samples tested positive for Klebsiella pneumoniae, we compared the analysis of virulence and resistance genes using metagenomics data to whole-genome sequencing of corresponding isolates obtained in culture. RESULTS Out of the 62 samples included, standard approaches and SMg yielded documentation in 80.6% and 96.8%, respectively. In 37.1% (23/62) of cases, both methods showed identical results, whereas in 43.5% (27/62) of cases, the samples were positive by both methods, but SMg found additional species in 88.9% (24/27), mostly anaerobes. When the standard approaches were negative, the SMg was able to detect microorganisms in 80.0% of cases (8/10). Overall, SMg identified significantly more microorganisms than culture (414 vs.105; p<0.05). K. pneumoniae genome analysis was able to detect resistance and virulence genes with a level of sensitivity depending on the depth of sequencing. DISCUSSION Overall, we showed that SMg had better performance in detecting and identifying microorganisms from LA samples and could help characterizing strain's resistome and virulome. Although still costly and requiring specific skills and expensive equipment, MGs methods are set to expand in the future.
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Affiliation(s)
- Hadrien Kimseng
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Geoffrey Rossi
- Department of Internal Medicine, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Maxime Danjean
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Bryan Jimenez-Araya
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Camille Chaligne
- Department of Internal Medicine, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Adrien Galy
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; Antimicrobial Stewardship Team, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France
| | - Bérénice Souhail
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; Antimicrobial Stewardship Team, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France
| | - Frédéric Bert
- Department of Microbiology, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Véronique Leflon
- Department of Microbiology, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Vincent Fihman
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | | | | | - Sarah Seng
- NGS Platform, IMRB Institute, Créteil, France
| | | | | | | | - Hervé Jacquier
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France
| | - Maxime Ronot
- Department of Radiology, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France
| | - Edouard Reizine
- Department of Radiology, Henri Mondor Hospital, AP-HP, Créteil, France
| | - Vincent Le Roy
- Department of Hepatology, Henri Mondor Hospital, AP-HP, Créteil, France
| | - Agnès Lefort
- Department of Internal Medicine, Beaujon Hospital, GHU AP-HP Nord-Université Paris Cité, Clichy, France; IAME, UMR1137, Université Paris-Cité, Paris, France
| | - Christophe Rodriguez
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; INSERM U955, IMRB Institute, Créteil, France; NGS Platform, IMRB Institute, Créteil, France
| | - Raphaël Lepeule
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; Antimicrobial Stewardship Team, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France
| | - Paul-Louis Woerther
- Department of Microbiology, Henri Mondor Hospital, AP-HP, University of Paris-Est, Créteil, France; EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est, Créteil, France; NGS Platform, IMRB Institute, Créteil, France.
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Li Z, Yuan Z, Cao H, Huan D, Qiu Y, Xia T, Shen J. A case report on Mycobacterium houstonense infection after total hip arthroplasty. BMC Infect Dis 2023; 23:722. [PMID: 37880617 PMCID: PMC10598912 DOI: 10.1186/s12879-023-08705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Mycobacterium houstonense is a category of rapidly growing mycobacteria that is gram-positive, acid-fast, polycrystalline, and non-spore-forming. There have been few reports of human infection caused by Mycobacterium houstonense worldwide. CASE PRESENTATION We present a case of chronic periprosthetic joint infection caused by Mycobacterium houstonense in an elderly female patient. The patient developed signs of infection after undergoing total hip arthroplasty. Despite receiving antibiotic treatment and revision surgery, the signs of infection recurred repeatedly. Multiple bacterial cultures during the treatment period were negative. Later, we identified the pathogenic bacteria Mycobacterium houstonense through mNGS testing, isolated the bacteria from the ultrasonically centrifuged fluid of the prosthesis and obtained drug sensitivity results. Finally, we performed a revision surgery and treated the patient with moxifloxacin and clindamycin. After treatment, the patient did not show signs of infection recurrence during 24 months of follow-up. CONCLUSION Through a relevant literature search, we believe that Mycobacterium houstonense may show higher sensitivity to amikacin and quinolone antibiotics. Additionally, clarifying occult infection sources through methods such as gene testing will improve the diagnosis and treatment of periprosthetic joint infection.
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Affiliation(s)
- ZhiPeng Li
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - ZhaoFeng Yuan
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - HuiLing Cao
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - DaWei Huan
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - Yue Qiu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - TianWei Xia
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China
| | - JiRong Shen
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing, 210000, Jiangsu, China.
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Baek YJ, Lee YJ, Lee JA, Kim JH, Kwon HM, Yeom JS, Park KK, Jeong SJ. Role of α-Defensin and the Microbiome in Prosthetic Joint Infection: A Prospective Cohort Study in Korea. J Clin Med 2023; 12:5964. [PMID: 37762905 PMCID: PMC10532201 DOI: 10.3390/jcm12185964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
The utility of α-defensin (AD), leukocyte esterase (LE) levels, and metagenomics sequencing as diagnostic tools for prosthetic joint infection (PJI) has been suggested, but there are few studies among the Asian population. This study aimed to evaluate the diagnostic performance of various biomarkers for PJI and the role of the microbiome in the synovial fluid of patients with prostheses. Patients with suspected knee PJI were enrolled, and their blood and synovial fluid were collected. The cases were classified into the PJI and non-PJI groups. Significant differences between the two groups were observed in the levels of AD (4698 µg/L vs. 296 µg/L, p < 0.001) and positivity for LE (62.5% vs. 21.1%, p = 0.01). AD had 94.4% sensitivity and 89.5% specificity for diagnosing PJI, whereas LE had 37.5% sensitivity and 100% specificity. Microbiome taxonomic profiling showed high sensitivity. The number of operational taxonomic units and the richness of the microbiome in the synovial fluid were higher in the non-PJI than in the PJI group. AD has shown encouraging results in the Asian population as a diagnostic biomarker for PJI, and LE can be used as a diagnostic adjunct. The bacterial richness of the synovial fluid is likely associated with infections.
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Affiliation(s)
- Yae Jee Baek
- Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul 04401, Republic of Korea;
| | - Youn-Jung Lee
- Division of Infectious Diseases, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung Ah Lee
- Division of Infectious Diseases, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung Ho Kim
- Division of Infectious Diseases, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyuck Min Kwon
- Department of Orthopedic Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Joon-Sup Yeom
- Division of Infectious Diseases, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Kwan Kyu Park
- Department of Orthopedic Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Su Jin Jeong
- Department of Orthopedic Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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Fisher CR, Mangalaparthi KK, Greenwood-Quaintance KE, Abdel MP, Pandey A, Patel R. Mass spectrometry-based proteomic profiling of sonicate fluid differentiates Staphylococcus aureus periprosthetic joint infection from non-infectious failure: A pilot study. Proteomics Clin Appl 2023; 17:e2200071. [PMID: 36938941 PMCID: PMC10509319 DOI: 10.1002/prca.202200071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/21/2023]
Abstract
PURPOSE This pilot study aimed to use proteomic profiling of sonicate fluid samples to compare host response during Staphylococcus aureus-associated periprosthetic joint infection (PJI) and non-infected arthroplasty failure (NIAF) and identify potential novel biomarkers differentiating the two. EXPERIMENTAL DESIGN In this pilot study, eight sonicate fluid samples (four from NIAF and four from S. aureus PJI) were studied. Samples were reduced, alkylated, and trypsinized overnight, followed by analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) on a high-resolution Orbitrap Eclipse mass spectrometer. MaxQuant software suite was used for protein identification, filtering, and label-free quantitation. RESULTS Principal component analysis of the identified proteins clearly separated S. aureus PJI and NIAF samples. Overall, 810 proteins were identified based on their detection in at least three out of four samples from each group; 35 statistically significant differentially abundant proteins (DAPs) were found (two-sample t-test p-values ≤0.05 and log2 fold-change values ≥2 or ≤-2). Gene ontology pathway analysis found that microbial defense responses, specifically those related to neutrophil activation, to be increased in S. aureus PJI compared to NIAF samples. CONCLUSION AND CLINICAL RELEVANCE Proteomic profiling of sonicate fluid using LC-MS/MS differentiated S. aureus PJI and NIAF in this pilot study. Further work is needed using a larger sample size and including non-S. aureus PJI and a diversty of NIAF-types.
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Affiliation(s)
- Cody R. Fisher
- Mayo Clinic Graduate School of Biomedical Sciences, Department of Immunology, Mayo Clinic, Rochester, Minnesota
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kiran K. Mangalaparthi
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Matthew P. Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Akhilesh Pandey
- Division of Clinical Biochemistry and Immunology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
- Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota
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Kato H, Hagihara M, Asai N, Umemura T, Hirai J, Yamagishi Y, Iwamoto T, Mikamo H. Comparison of microbial detection rates in microbial culture methods versus next-generation sequencing in patients with prosthetic joint infection: a systematic review and meta-analysis. J Orthop Surg Res 2023; 18:604. [PMID: 37587529 PMCID: PMC10428596 DOI: 10.1186/s13018-023-03973-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/03/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Accurate diagnosis of prosthetic joint infection (PJI) enables early and effective treatment. However, there is currently no gold standard test for microbial detection of PJI and traditional synovial fluid culture is relatively insensitive. Recently, it has been reported that sonicating fluid culture and next-generation sequencing (NGS) improve microbial detection rates. Hence, we performed a systematic review and meta-analysis to compare microbial detection rates in microbial culture methods with and without sonication versus NGS. METHODS We systematically searched EMBASE, PubMed, Scopus, CINAHL, and Ichushi databases and other sources (previous reviews) until August 2022. We evaluated the detection rates of pathogens in NGS and microbial cultures using samples of synovial or sonicated fluid. RESULTS Of the 170 citations identified for screening, nine studies were included. Pooled analysis indicated that NGS had the highest detection rate among the microbial detection methods (NGS vs. sonicated, odds ratios [OR] 5.09, 95% confidential interval [CI] 1.67-15.50; NGS vs. synovial, OR 4.52, 95% CI 2.86-7.16). Sonicated fluid culture showed a higher detection rate than synovial fluid culture (OR 2.11, 95% CI 1.23-3.62). CONCLUSION NGS might be useful as a screening tool for culture-negative patients. In clinical settings, sonicated fluid culture is a practical method for diagnosing PJI.
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Affiliation(s)
- Hideo Kato
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
- Department of Pharmacy, Mie University Hospital, Mie, Japan
- Division of Clinical Medical Science, Department of Clinical Pharmaceutics, Mie University Graduate School of Medicine, Mie, Japan
| | - Mao Hagihara
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
- Department of Molecular Epidemiology and Biomedical Sciences, Aichi Medical University Hospital, Aichi, Japan
| | - Nobuhiro Asai
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Takumi Umemura
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Jun Hirai
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Yuka Yamagishi
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Takuya Iwamoto
- Department of Pharmacy, Mie University Hospital, Mie, Japan
- Division of Clinical Medical Science, Department of Clinical Pharmaceutics, Mie University Graduate School of Medicine, Mie, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute, Aichi, 480-1195, Japan.
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Li H, Fu J, Erlong N, Li R, Xu C, Hao L, Chen J, Chai W. Characterization of periprosthetic environment microbiome in patients after total joint arthroplasty and its potential correlation with inflammation. BMC Infect Dis 2023; 23:423. [PMID: 37349686 DOI: 10.1186/s12879-023-08390-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/08/2023] [Indexed: 06/24/2023] Open
Abstract
AIMS Periprosthetic joint infection (PJI) is one of the most serious complications after total joint arthroplasty (TJA) but the characterization of the periprosthetic environment microbiome after TJA remains unknown. Here, we performed a prospective study based on metagenomic next-generation sequencing to explore the periprosthetic microbiota in patients with suspected PJI. METHODS We recruited 28 patients with culture-positive PJI, 14 patients with culture-negative PJI, and 35 patients without PJI, which was followed by joint aspiration, untargeted metagenomic next-generation sequencing (mNGS), and bioinformatics analysis. Our results showed that the periprosthetic environment microbiome was significantly different between the PJI group and the non-PJI group. Then, we built a "typing system" for the periprosthetic microbiota based on the RandomForest Model. After that, the 'typing system' was verified externally. RESULTS We found the periprosthetic microbiota can be classified into four types generally: "Staphylococcus type," "Pseudomonas type," "Escherichia type," and "Cutibacterium type." Importantly, these four types of microbiotas had different clinical signatures, and the patients with the former two microbiota types showed obvious inflammatory responses compared to the latter ones. Based on the 2014 Musculoskeletal Infection Society (MSIS) criteria, clinical PJI was more likely to be confirmed when the former two types were encountered. In addition, the Staphylococcus spp. with compositional changes were correlated with C-reactive protein levels, the erythrocyte sedimentation rate, and the synovial fluid white blood cell count and granulocyte percentage. CONCLUSIONS Our study shed light on the characterization of the periprosthetic environment microbiome in patients after TJA. Based on the RandomForest model, we established a basic "typing system" for the microbiota in the periprosthetic environment. This work can provide a reference for future studies about the characterization of periprosthetic microbiota in periprosthetic joint infection patients.
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Affiliation(s)
- Hao Li
- Medical School of Chinese PLA, Beijing, People's Republic of China
- Department of Orthopedic Surgery, The First Medical Center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China
| | - Jun Fu
- Department of Orthopedic Surgery, The First Medical Center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China
| | - Niu Erlong
- Department of Orthopedics, 305 Hospital of PLA, Beijing, People's Republic of China
| | - Rui Li
- Senior Department of Orthopedics, Fourth Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Chi Xu
- Department of Orthopedic Surgery, The First Medical Center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China
| | - Libo Hao
- Department of Orthopedic Surgery, The First Medical Center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China
| | - Jiying Chen
- Department of Orthopedic Surgery, The First Medical Center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China.
| | - Wei Chai
- Department of Orthopedic Surgery, The First Medical Center, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, People's Republic of China.
- Senior Department of Orthopedics, Fourth Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China.
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Bos MP, van Houdt R, Poort L, van der Stel AX, Peters EJ, Saouti R, Savelkoul P, Budding AE. Rapid Diagnostics of Joint Infections Using IS-Pro. J Clin Microbiol 2023; 61:e0015423. [PMID: 37154734 PMCID: PMC10281151 DOI: 10.1128/jcm.00154-23] [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: 02/13/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
Diagnosis of bone and joint infections (BJI) relies on microbiological culture which has a long turnaround time and is challenging for certain bacterial species. Rapid molecular methods may alleviate these obstacles. Here, we investigate the diagnostic performance of IS-pro, a broad-scope molecular technique that can detect and identify most bacteria to the species level. IS-pro additionally informs on the amount of human DNA present in a sample, as a measure of leukocyte levels. This test can be performed in 4 h with standard laboratory equipment. Residual material of 591 synovial fluid samples derived from native and prosthetic joints from patients suspected of joint infections that were sent for routine diagnostics was collected and subjected to the IS-pro test. Bacterial species identification as well as bacterial load and human DNA load outcomes of IS-pro were compared to those of culture. At sample level, percent positive agreement (PPA) between IS-pro and culture was 90.6% (95% CI 85.7- to 94%) and negative percent agreement (NPA) was 87.7% (95% CI 84.1 to 90.6%). At species level PPA was 80% (95% CI 74.3 to 84.7%). IS-pro yielded 83 extra bacterial detections over culture for which we found supporting evidence for true positivity in 40% of the extra detections. Missed detections by IS-pro were mostly related to common skin species in low abundance. Bacterial and human DNA signals measured by IS-pro were comparable to bacterial loads and leukocyte counts reported by routine diagnostics. We conclude that IS-pro showed an excellent performance for fast diagnostics of bacterial BJI.
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Affiliation(s)
| | - Robin van Houdt
- Department of Medical Microbiology & Infection Control, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | | | - Edgar J. Peters
- Amsterdam UMC, location Vrije Universiteit Amsterdam, Infectious Diseases, Amsterdam Infection & Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Rachid Saouti
- Department of Orthopedic Surgery, Amsterdam UMC, Amsterdam Movement Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul Savelkoul
- Department of Medical Microbiology & Infection Control, Amsterdam UMC, location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology, Infectious Diseases & Infection Prevention, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht UMC, Maastricht, The Netherlands
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Huang C, Huang Y, Wang Z, Lin Y, Li Y, Chen Y, Chen X, Zhang C, Li W, Zhang W, Fang X, Huang Z. Multiplex PCR-based next generation sequencing as a novel, targeted and accurate molecular approach for periprosthetic joint infection diagnosis. Front Microbiol 2023; 14:1181348. [PMID: 37275128 PMCID: PMC10232910 DOI: 10.3389/fmicb.2023.1181348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/27/2023] [Indexed: 06/07/2023] Open
Abstract
Objectives Periprosthetic joint infection (PJI) diagnosis remains challenging, and the identification of the causative microorganism is, by far, the most important aspect. Here, we use multiple PCR-based targeted next-generation sequencing (tNGS) to detect pathogens in PJI. To explore 1. the ability of targeted next-generation sequencing (tNGS) to detect pathogens in PJI; 2. the consistency of tNGS, metagenomic NGS (mNGS), and culture results; and 3. the ability of tNGS to detect drug resistance genes in PJI. Methods PJI was diagnosed according to the Musculoskeletal Infection Society (MSIS) criteria. The microorganisms were detected by culture, mNGS and tNGS to compare the diagnostic effectiveness of the three methods for PJI and to compare their consistency in detecting microorganisms. Drug resistance genes were detected using tNGS. The costs and turnaround times of mNGS and tNGS were compared. Results Forty-three patients with PJI, 21 patients without PJI and 10 negative control cases were included. The culture, tNGS, and mNGS sensitivities for PJI diagnosis were 74.41%, 88.37%, and 93.02%, respectively, with no significant differences. The specificities were 90.48%, 95.24%, and 95.24%, respectively, with no significant differences. tNGS detected drug resistance genes in 37.5% of culture-positive PJIs. tNGS was superior to mNGS for turnaround time (14.5 h vs. 28 h) and cost ($150 vs. $260). Conclusions tNGS can effectively identify PJI pathogens and may provide drug resistance information, while tNGS is superior to mNGS regarding cost and turnaround time. A multidisciplinary, multi-technology based algorithm to diagnose PJI is appropriate. Highlights 298 microorganisms and 86 drug resistance genes were included in the tNGS panel.Diagnostic efficacy of tNGS is not inferior to that of commonly used indicators.tNGS is superior to mNGS in cost and turnaround time.
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Affiliation(s)
- Changyu Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ying Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ziwen Wang
- Fujian Medical University, Fuzhou, China
| | - Yiming Lin
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yongbin Li
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yang Chen
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xiaoqing Chen
- Department of Orthopedic Surgery, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Chaofan Zhang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wenming Zhang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xinyu Fang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Zida Huang
- Department of Orthopaedic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Fujian Provincial Institute of Orthopedics, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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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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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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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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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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Lacasse M, Derolez S, Bonnet E, Amelot A, Bouyer B, Carlier R, Coiffier G, Cottier JP, Dinh A, Maldonado I, Paycha F, Ziza JM, Bemer P, Bernard L. 2022 SPILF - Clinical Practice guidelines for the diagnosis and treatment of disco-vertebral infection in adults. Infect Dis Now 2023; 53:104647. [PMID: 36690329 DOI: 10.1016/j.idnow.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/12/2022] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
These guidelines are an update of those made in 2007 at the request of the French Society of Infectious Diseases (SPILF, Société de Pathologie Infectieuse de Langue Française). They are intended for use by all healthcare professionals caring for patients with disco-vertebral infection (DVI) on spine, whether native or instrumented. They include evidence and opinion-based recommendations for the diagnosis and management of patients with DVI. ESR, PCT and scintigraphy, antibiotic therapy without microorganism identification (except for emergency situations), therapy longer than 6 weeks if the DVI is not complicated, contraindication for spinal osteosynthesis in a septic context, and prolonged dorsal decubitus are no longer to be done in DVI management. MRI study must include exploration of the entire spine with at least 2 orthogonal planes for the affected level(s). Several disco-vertebral samples must be performed if blood cultures are negative. Short, adapted treatment and directly oral antibiotherapy or early switch from intravenous to oral antibiotherapy are recommended. Consultation of a spine specialist should be requested to evaluate spinal stability. Early lifting of patients is recommended.
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Affiliation(s)
- M Lacasse
- Medecine Interne et Maladies Infectieuses, 2 Bd Tonnelé, CHU Bretonneau, 37044 Tours Cedex 09, France
| | - S Derolez
- Rhumatologie, 125 rue de Stalingrad, CHU Avicenne, 93000 Bobigny, France
| | - E Bonnet
- Maladies Infectieuses, Pl. Dr Baylac, CHU Purpan, 31000 Toulouse, France.
| | - A Amelot
- Neurochirurgie, 2 Bd Tonnelé, CHU Bretonneau, 37044 Tours Cedex 09, France
| | - B Bouyer
- Chirurgie orthopédique et traumatologique, CHU de Bordeaux, Place Amélie Raba-léon, 33076 Bordeaux, France
| | - R Carlier
- Imagerie, Hôpital Raymond Poincaré, 104 Bd R Poincaré, 92380 Garches, France
| | - G Coiffier
- Rhumatologie, GH Rance-Emeraude, Hôpital de Dinan, 22100 Dinan, France
| | - J P Cottier
- Radiologie, 2 Bd Tonnelé, CHU Bretonneau, 37044 Tours Cedex 09, France
| | - A Dinh
- Maladies Infecteiuses, CHU Raymond Poicaré, 92380 Garches, France
| | - I Maldonado
- Radiologie, 2 Bd Tonnelé, CHU Bretonneau, 37044 Tours Cedex 09, France
| | - F Paycha
- Médecine Nucléaire, Hôpital Lariboisière, 2 rue Ambroise Paré 75010 Paris, France
| | - J M Ziza
- Rhumatologie et Médecine Interne. GH Diaconesses Croix Saint Simon, 75020 Paris, France
| | - P Bemer
- Microbiologie, CHU de Nantes, 1 Place A. Ricordeau, Nantes 44000 Cedex 1, France
| | - L Bernard
- Medecine Interne et Maladies Infectieuses, 2 Bd Tonnelé, CHU Bretonneau, 37044 Tours Cedex 09, France
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Xu J, Zhou P, Liu J, Zhao L, Fu H, Han Q, Wang L, Wu W, Ou Q, Ma Y, He J. Utilizing Metagenomic Next-Generation Sequencing (mNGS) for Rapid Pathogen Identification and to Inform Clinical Decision-Making: Results from a Large Real-World Cohort. Infect Dis Ther 2023; 12:1175-1187. [PMID: 36988865 PMCID: PMC10147866 DOI: 10.1007/s40121-023-00790-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
INTRODUCTION Clinical metagenomic next-generation sequencing (mNGS) has proven to be a powerful diagnostic tool in pathogen detection. However, its clinical utility has not been thoroughly evaluated. METHODS In this single-center prospective study at the First Affiliated Hospital of Soochow University, a total of 228 samples from 215 patients suspected of having acute or chronic infections between June 2018 and December 2018 were studied. Samples that met the mNGS quality control (QC) criteria (N = 201) were simultaneously analyzed using conventional tests (CTs), including multiple clinical microbiological tests and real-time PCR (if applicable). RESULTS Pathogen detection results of mNGS in the 201 QC-passed samples were compared to CTs and exhibited a sensitivity of 98.8%, specificity of 38.5%, and accuracy of 87.1%. Specifically, 109 out of 160 (68.1%) CT+/mNGS+ samples exhibited concordant results at the species/genus level, 25 samples (15.6%) showed overlapping results, while the remaining 26 samples (16.3%) had discordant results between the CT and mNGS assays. In addition, mNGS could identify pathogens at the species level, whereas only the genera of some pathogens could be identified by CT. In this cohort, mNGS results were used to guide treatment plans in 24 out of 41 cases that had available follow-up information, and the symptoms were improved in over 70% (17/24) of them. CONCLUSION Our data demonstrated the analytic performance of our mNGS pipeline for pathogen detection using a large clinical cohort and strongly supports the notion that in clinical practice, mNGS represents a valuable supplementary tool to CTs to rapidly determine etiological factors of various types of infection and to guide treatment decision-making.
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Affiliation(s)
- Jie Xu
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China
| | - Peng Zhou
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Jia Liu
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Lina Zhao
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Hailong Fu
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China
| | - Qingzhen Han
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Lin Wang
- Center of Translational Medicine and Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215028, China
| | - Weiwei Wu
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Qiuxiang Ou
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Yutong Ma
- Dinfectome Inc., NanjingJiangsu, 210000, China
| | - Jun He
- Clinical Laboratory Center, The First Affiliated Hospital of Soochow University, Suzhou, 215031, China.
- HLA Laboratory of Jiangsu Institute of Hematology, Collaborative Innovation Center of Hematology, The First Affiliated Hospital of Soochow University, 13/F (West), Hospital Comprehensive Building, No.899 Ping Hai Road, Suzhou, 215031, Jiangsu, China.
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Gao L, Yang T, Zhang X, Lei W, Huang JA. Rapid detection of pulmonary nocardiosis by metagenomic next generation sequencing. Diagn Microbiol Infect Dis 2023; 106:115928. [PMID: 37001227 DOI: 10.1016/j.diagmicrobio.2023.115928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/01/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023]
Abstract
We retrospectively analyzed 3 cases of pulmonary nocardiosis. Patients were identified by metagenomic next generation sequencing (mNGS) in the First Affiliated Hospital of Soochow University, from January 2019 to April 2022. All patients had underlying diseases, and were in immunocompromised state, with membranous nephropathy, acute lymphoblastic leukemia (ALL), and systemic lupus erythematosus (SLE), respectively. Symptoms common to all cases included fever, cough and expectoration. Chest computed tomography (CT) presented patchy shadows or nodules, with or without cavitation lesions, or pleural effusion. mNGS detected Nocardia spp. via bronchoalveolar lavage fluid (BALF) or blood samples from patients. All the patients were discharged with recovery after using the trimethoprim-sulfamethoxazole (TMP-SMX) and remained without evidence of disease during regular follow-ups. mNGS may be a tool for rapid and accurate detection and identification of pulmonary nocardiosis, but interpreting the mNGS results should be more cautious because the mNGS assay can also detect colonization.
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Wang C, Hu J, Gu Y, Wang X, Chen Y, Yuan W. Application of next-generation metagenomic sequencing in the diagnosis and treatment of acute spinal infections. Heliyon 2023; 9:e13951. [PMID: 36879954 PMCID: PMC9984843 DOI: 10.1016/j.heliyon.2023.e13951] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Objectives The purpose of this study was to verify the value of metagenomic next-generation sequencing (mNGS) in detecting the pathogens causing acute spinal infection by reviewing the results of mNGS in 114 patients. Methods A total of 114 patients were included from our hospital. Samples (tissue/blood) were sent for mNGS detection, and the remaining samples were sent to the microbiology laboratory for pathogen culture, smear, histopathological analysis, and other tests. Patients' medical records were reviewed to determine their rates of detection, time needed, guidance for antibiotic treatment and clinical outcomes. Results mNGS showed a satisfying diagnostic positive percent agreement of 84.91% (95% confidence interval (CI): 6.34%-96.7%), compared to 30.19% (95% CI: 21.85%-39.99%) for culture and 43.40% (95% CI: 31.39%-49.97%) for conventional methods (p < 0.0125), and mNGS was found positive in 46 culture and smear negative samples. The time required for pathogen identification using mNGS ranged from 29 h to 53 h, which showed an advantage over culture (90.88 ± 8.33 h; P < 0.05). mNGS also played an important role in optimizing antibiotic regimens in patients with negative results obtained using conventional methods. The treatment success rate (TSR) of patients using mNGS-guided antibiotic regimens (20/24, 83.33%) was significantly higher than that of patients using empirical antibiotics (13/23, 56.52%) (P < 0.0001). Conclusions mNGS shows promising potential in the pathogenic diagnosis of acute spinal infections and may enable clinicians to make more timely and effective adjustments to antibiotic regimens.
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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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Li X, Yang L, Li D, Yang X, Wang Z, Chen M, Wu F, Dou X, Niu M, Qi H, Deng T, Xia H, Wang D. Diagnosis of Neurological Infections in Pediatric Patients from Cell-Free DNA Specimens by Using Metagenomic Next-Generation Sequencing. Microbiol Spectr 2023; 11:e0253022. [PMID: 36651744 PMCID: PMC9927296 DOI: 10.1128/spectrum.02530-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
Central nervous system (CNS) infections can cause significant morbidity and mortality, especially in children. Rapid and accurate pathogenic detection in suspected CNS infections is essential for disease control at the early stage of infection. To evaluate the performance of metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) in pediatric patients, we retrospectively analyzed the efficiency of cfDNA mNGS in children with CNS infections (n = 257) or noninfectious neurological disorders (n = 81). The CSF samples of 124 random subjects were used to evaluate the accuracy between mNGS of cfDNA and whole-cell DNA (wcDNA). In total, cfDNA mNGS detected a wide range of microbes with a detection rate of 71.0%, and the sensitivity and total coincidence rate with clinical diagnosis reached 68.9% and 67.5%, respectively. Compared with wcDNA mNGS, cfDNA mNGS had a higher efficacy in detecting viruses (66 versus 13) and Mycobacterium (7 versus 1), with significantly higher reads per million. The dominant causative pathogens were bacteria and viruses in CNS infections, but these presented with different pathogen spectra in different age categories. The best timing for the mNGS test ranged from 1 to 6 days after the start of anti-infection therapy, and the earlier mNGS started, the better was identification of bacterial CNS infections. This study emphasized that cfDNA mNGS had overall superiority to conventional methods on causative pathogen detection in pediatric CNS infections, and it was even better than wcDNA mNGS. Furthermore, research needs to be better validated in large-scale clinical trials to improve the clinical applications of cfDNA mNGS. IMPORTANCE Our study emphasized that cfDNA mNGS had overall superiority to conventional methods on causative pathogen detection in CNS-infected children, and it was even better than wcDNA mNGS. cfDNA mNGS detected a wide range of pathogens with a high total coincidence rate (67.5%) against clinical diagnosis. The best timing for cfDNA mNGS detection ranged from 1 to 6 days, rather than 0 days, after the start of empirical anti-infection therapy. The earlier mNGS started, the better the identifications of bacterial CNS infections. To the best of our knowledge, this research is the first report evaluating the clinical utility of mNGS with different methods (cfDNA versus wcDNA) of extracting DNA from CSF specimens in diagnosing pediatric CNS infections. Meanwhile, this is the largest cohort study that has evaluated the performance of mNGS using cfDNA from CSF specimens in pediatric patients with CNS infections.
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Affiliation(s)
- Xia Li
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Le Yang
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Dongjing Li
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Xuying Yang
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Zhijing Wang
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Mengyi Chen
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Fang Wu
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Xiangjun Dou
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Mengmeng Niu
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - HongYan Qi
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Ting Deng
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
| | - Han Xia
- Department of Scientific Affaires, Hugobiotech Co., Ltd., Beijing, China
| | - Dong Wang
- Department of Pediatric Neurology, Xi’an Children’s hospital, Xi’an City, Shaanxi Province, China
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Hong HL, Flurin L, Thoendel MJ, Wolf MJ, Abdel MP, Greenwood-Quaintance KE, Patel R. Targeted Versus Shotgun Metagenomic Sequencing-based Detection of Microorganisms in Sonicate Fluid for Periprosthetic Joint Infection Diagnosis. Clin Infect Dis 2023; 76:e1456-e1462. [PMID: 35944127 PMCID: PMC10169413 DOI: 10.1093/cid/ciac646] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/15/2022] [Accepted: 08/08/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is increasingly used for periprosthetic joint infection (PJI) diagnosis, but its clinical utility is poorly defined. Shotgun metagenomic sequencing (sNGS) has been reported to identify PJI pathogens undetected by culture in sonicate fluid. However, sNGS is complex and costly. Here, 16S ribosomal RNA (rRNA) gene-based targeted metagenomic sequencing (tNGS) was compared to sNGS of sonicate fluid for microbial detection and identification in patients with total hip arthroplasty (THA) and total knee arthroplasty (TKA) failure. METHODS A convenience sample of sonicate fluids derived from patients who had undergone THA or TKA removal, enriched with culture negative PJI cases, was tested. Samples had been previously tested by sNGS. For tNGS, samples were extracted, amplified by polymerase chain reaction targeting the V1 to V3 regions of the 16S rRNA gene, and sequenced on an Illumina MiSeq. RESULTS A total of 395 sonicate fluids, including 208 from subjects with PJI, were studied. Compared with sonicate fluid culture, tNGS had higher positive percent agreement (72.1 vs 52.9%, P < .001), detecting potential pathogens in 48.0% of culture-negative PJIs. There was no difference between the positive percent agreement of tNGS (72.1%) and sNGS (73.1%, P = .83). CONCLUSIONS 16S rRNA gene-based tNGS is a potential diagnostic tool for PJI pathogen identification in sonicate fluid from failed THAs and TKAs in culture-negative cases, with similar performance characteristics to sNGS.
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Affiliation(s)
- Hyo-Lim Hong
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Internal Medicine, Daegu Catholic University School of Medicine, Daegu, Republic of Korea
| | - Laure Flurin
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Intensive Care, University Hospital of Guadeloupe, Pointe-à-Pitre, France
| | - Matthew J Thoendel
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J Wolf
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Kerryl E Greenwood-Quaintance
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Tarabichi S, Chen AF, Higuera CA, Parvizi J, Polkowski GG. 2022 American Association of Hip and Knee Surgeons Symposium: Periprosthetic Joint Infection. J Arthroplasty 2023:S0883-5403(23)00065-7. [PMID: 36738863 DOI: 10.1016/j.arth.2023.01.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/06/2023] Open
Abstract
Periprosthetic joint infection (PJI) is the leading cause of failure in patients undergoing total joint arthroplasty. This article is a brief summary of a symposium on PJI that was presented at the annual AAHKS meeting. It will provide an overview of current technqiues in the prevention, diagnosis, and management of PJI. It will also highlight emerging technologies in this setting.
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Affiliation(s)
- Saad Tarabichi
- Rothman Orthopaedic Institute at Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Antonia F Chen
- Department of Orthopaedic Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Carlos A Higuera
- Levitetz Department of Orthopaedic Surgery, Cleveland Clinic Florida, Weston, Florida
| | - Javad Parvizi
- Rothman Orthopaedic Institute at Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Gregory G Polkowski
- Department of Orthopaedic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
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Fisher CR, Patel R. Profiling the Immune Response to Periprosthetic Joint Infection and Non-Infectious Arthroplasty Failure. Antibiotics (Basel) 2023; 12:296. [PMID: 36830206 PMCID: PMC9951934 DOI: 10.3390/antibiotics12020296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Arthroplasty failure is a major complication of joint replacement surgery. It can be caused by periprosthetic joint infection (PJI) or non-infectious etiologies, and often requires surgical intervention and (in select scenarios) resection and reimplantation of implanted devices. Fast and accurate diagnosis of PJI and non-infectious arthroplasty failure (NIAF) is critical to direct medical and surgical treatment; differentiation of PJI from NIAF may, however, be unclear in some cases. Traditional culture, nucleic acid amplification tests, metagenomic, and metatranscriptomic techniques for microbial detection have had success in differentiating the two entities, although microbiologically negative apparent PJI remains a challenge. Single host biomarkers or, alternatively, more advanced immune response profiling-based approaches may be applied to differentiate PJI from NIAF, overcoming limitations of microbial-based detection methods and possibly, especially with newer approaches, augmenting them. In this review, current approaches to arthroplasty failure diagnosis are briefly overviewed, followed by a review of host-based approaches for differentiation of PJI from NIAF, including exciting futuristic combinational multi-omics methodologies that may both detect pathogens and assess biological responses, illuminating causes of arthroplasty failure.
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Affiliation(s)
- Cody R. Fisher
- Mayo Clinic Graduate School of Biomedical Sciences, Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
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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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Chen H, Liang Y, Wang R, Wu Y, Zhang X, Huang H, Yu X, Hong M, Yang J, Liao K, Xu H, Liu M, Chen P, Chen Y. Metagenomic next-generation sequencing for the diagnosis of Pneumocystis jirovecii Pneumonia in critically pediatric patients. Ann Clin Microbiol Antimicrob 2023; 22:6. [PMID: 36647095 PMCID: PMC9841943 DOI: 10.1186/s12941-023-00555-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
OBJECTIVE The aim of this study was to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) for the diagnosis of Pneumocystis jirovecii Pneumonia (PCP) in critically pediatric patients. METHODS Seventeen critically pediatric patients with PCP and sixty patients diagnosed with non-PCP pneumonia who were admitted in pediatric intensive care unit between June 2018 and July 2021 were enrolled. Conventional methods and mNGS for detecting Pneumocystis jirovecii (P. jirovecii) were compared. The patients' demographics, comorbidities, laboratory test results, antibiotic treatment response and 30 day mortality were analyzed. RESULT The mNGS showed a satisfying diagnostic performance with a sensitivity of 100% in detecting P. jirovecii compared with Gomori methenamine silver staining (5.9%), serum (1,3)-β-D-glucan (86.7%) and and LDH (55.6%). The diagnostic specificity of mNGS for PCP was higher than that of serum BDG (56.7%) and LDH (71.4%). In PCP group, over one thirds' cases had mixed infections. Compared with survivors, non-survivors had higher stringently mapped read numbers (SMRNs) in bronchoalveolar lavage fluid (BALF) sample (P < 0.05), suggesting SMRNs were closely associated with the severity of response. The detection for P. jirovecii by mNGS both in BALF and blood samples reached a concordance rate of 100%, and the SMRNs in the BALF were remarkably higher than that in blood samples. Initial antimicrobial treatment was modified in 88.2% of PCP patients based on the mNGS results. CONCLUSION The mNGS is a potential and efficient technology in diagnosing PCP and shows a satisfying performance in the detection of co-pathogens. Both blood and BALF samples for mNGS are suggested for the presumptive diagnosis of PCP.
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Affiliation(s)
- Hengxin Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Yujian Liang
- Department of Pediatric Intensive Care Unit, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Ruizhi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Yijie Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China
| | - Xiaoyun Zhang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China
| | - Hao Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Xuegao Yu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Mengzhi Hong
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Juhua Yang
- Vision Medicals Co., Ltd, Guangzhou, China
| | - Kang Liao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Hongxu Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Min Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
| | - Yili Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China.
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Fisher CR, Krull JE, Bhagwate A, Masters T, Greenwood-Quaintance KE, Abdel MP, Patel R. Sonicate Fluid Cellularity Predicted by Transcriptomic Deconvolution Differentiates Infectious from Non-Infectious Arthroplasty Failure. J Bone Joint Surg Am 2023; 105:63-73. [PMID: 36574631 PMCID: PMC10137834 DOI: 10.2106/jbjs.22.00605] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Although cellularity is traditionally assessed morphologically, deep sequencing approaches being used for microorganism detection may be able to provide information about cellularity. We hypothesized that cellularity predicted using CIBERSORTx (Stanford University), a transcriptomic-based cellular deconvolution tool, would differentiate between infectious and non-infectious arthroplasty failure. METHODS CIBERSORTx-derived cellularity profiles of 93 sonicate fluid samples, including 53 from subjects who underwent failed arthroplasties due to periprosthetic joint infection (PJI) (abbreviated for the purpose of this study as PJIF) and 40 from subjects who had undergone non-infectious arthroplasty failure (abbreviated NIAF) that had been subjected to bulk RNA sequencing were evaluated. RESULTS Samples from PJIF and NIAF subjects were differentially clustered by principal component analysis based on the cellularity profile. Twelve of the 22 individual predicted cellular fractions were differentially expressed in the PJIF cases compared with the NIAF cases, including increased predicted neutrophils (mean and standard error, 9.73% ± 1.06% and 0.81% ± 0.60%), activated mast cells (17.12% ± 1.51% and 4.11% ± 0.44%), and eosinophils (1.96% ± 0.37% and 0.42% ± 0.21%), and decreased predicted M0 macrophages (21.33% ± 1.51% and 39.75% ± 2.45%), M2 macrophages (3.56% ± 0.52% and 8.70% ± 1.08%), and regulatory T cells (1.57% ± 0.23% and 3.20% ± 0.34%). The predicted total granulocyte fraction was elevated in the PJIF cases (32.97% ± 2.13% and 11.76% ± 1.61%), and the samples from the NIAF cases had elevated predicted total macrophage and monocyte (34.71% ± 1.71% and 55.34% ± 2.37%) and total B cell fractions (5.89% ± 0.30% and 8.62% ± 0.86%). Receiver operating characteristic curve analysis identified predicted total granulocytes, neutrophils, and activated mast cells as highly able to differentiate between the PJIF cases and the NIAF cases. Within the PJIF cases, the total granulocyte, total macrophage and monocyte, M0 macrophage, and M2 macrophage fractions were differentially expressed in Staphylococcus aureus compared with Staphylococcus epidermidis -associated samples. Within the NIAF cases, the predicted total B cell, naïve B cell, plasma cell, and M2 macrophage fractions were differentially expressed among different causes of failure. CONCLUSIONS CIBERSORTx can predict the cellularity of sonicate fluid using transcriptomic data, allowing for the evaluation of the underlying immune response during the PJIF and NIAF cases, without a need to phenotypically assess cell composition.
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Affiliation(s)
- Cody R Fisher
- Department of Immunology, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota.,Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jordan E Krull
- Department of Immunology, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota
| | - Aditya Bhagwate
- Department of Quantitative Sciences, Mayo Clinic, Rochester, Minnesota
| | - Thao Masters
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kerryl E Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matthew P Abdel
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Division of Public Health, Infectious Diseases and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota
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Meng LN, Li G, Yuan HX, Feng XC, Liu F, Zhang SL. Utility of metagenomics next-generation sequencing in the diagnosis and treatment of severe infectious diseases in the intensive care unit. Technol Health Care 2023; 31:1887-1899. [PMID: 37302051 DOI: 10.3233/thc-220856] [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] [Indexed: 06/12/2023]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is a new method that combines high-throughput sequencing and bioinformatics analysis. However, it has not become as popular due to the limited testing equipment and high costs and lack of family awareness with not much relevant intensive care unit (ICU) research data. OBJECTIVE To explore the clinical use and value of metagenomics next-generation sequencing (mNGS) in patients with sepsis in the ICU. METHODS We conducted a retrospective analysis of 102 patients with sepsis admitted to the ICU of Peking University International Hospital from January 2018 to January 2022. Based on whether mNGS was performed, the identified patients were divided into the observation group (n= 51) and the control group (n= 51), respectively. Routine laboratory tests, including routine blood test, C-reactive protein, procalcitonin, and culture of suspicious lesion specimens were performed in both groups within 2 hours after admission to the ICU, while mNGS tests were performed in the observation group. Patients in both groups were routinely given initial anti-infective, anti-shock, and organ support treatment. Antibiotic regimens were optimized in a timely manner according to the etiological results. Relevant clinical data were collected. RESULTS The testing cycle of mNGS was shorter than that of the conventional culture (30.79 ± 4.01 h vs. 85.38 ± 9.94 h, P< 0.001), while the positive rate of mNGS was higher than that of the conventional culture (82.35% vs. 45.1%, P< 0.05), with obvious superiority in the detection of viruses and fungus. There were significant differences in the optimal time of antibiotics (48 h vs.100 h) and length of ICU stay (11 d vs. 16 d) between the observation group and control group (P< 0.01) respectively, with no difference in 28-day mortality (33.3% vs. 41.2%, P> 0.05). CONCLUSION mNGS is useful in the detection of sepsis-causing pathogens in the ICU with the advantages of short testing time and high positive rate. There was no difference in the 28-day outcome between the two groups, which may be related to other confounding factors such as small sample size. Additional studies with extended sample size are needed.
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50
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Jia K, Huang S, Shen C, Li H, Zhang Z, Wang L, Zhao G, Wu Z, Lin Y, Xia H, Tang M, Yang H, Hu H. Enhancing urinary tract infection diagnosis for negative culture patients with metagenomic next-generation sequencing (mNGS). Front Cell Infect Microbiol 2023; 13:1119020. [PMID: 36936777 PMCID: PMC10020507 DOI: 10.3389/fcimb.2023.1119020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a promising technology that allows unbiased pathogen detection and is increasingly being used for clinical diagnoses. However, its application in urinary tract infection (UTI) is still scarce. Methods The medical records of 33 patients with suspected UTI who were admitted to the Second Hospital of Tianjin Medical University from March 2021 to July 2022 and received urine mNGS were retrospectively analyzed. The performance of mNGS and conventional urine culture in diagnosing infection and identifying causative organisms was compared, and the treatment effects were evaluated in terms of changes in urinalyses and urinary symptoms. Results In the detection of bacteria and fungi, mNGS detected at least one pathogen in 29 (87.9%) cases, including 19 (57.6%) with positive mNGS but negative culture results and 10 (30.3%) with both mNGS and culture positive results. The remaining 4 (12.1%) patients were negative by both tests. Overall, mNGS performed better than culture (87.9% vs. 30.3%, P < 0.001). Within the 10 double-positive patients, mNGS matched culture results exactly in 5 cases, partially in 4 cases, and not at all in 1 case. In addition, mNGS detected a broader pathogen spectrum, detecting 26 species compared to only 5 species found in culture. The most abundant bacteria detected by mNGS was Escherichia coli, detected in 9 (27.2%) patients. All anaerobic bacteria, Mycobacterium Tuberculosis and all mixed pathogens were detected by mNGS. The final clinical diagnosis of UTI was made in 25 cases, and the sensitivity of mNGS was significantly higher than culture (100.0% vs 40.0%; P < 0.001) when using the diagnosis as a reference standard; the positive predictive value, negative predictive value and specificity were 86.2%, 100% and 50.0%, respectively. Importantly, targeted antibiotic therapy based on mNGS resulted in significant improvement in urinalyses and urinary symptoms in patients. Conclusions mNGS is a technology that has shown clear advantages over culture, particularly in the context of mixed infections and UTIs that are difficult to diagnose and treat. It helps to improve the detection of pathogens, guide changes in treatment strategies, and is an effective complement to urine culture.
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Affiliation(s)
- Kaipeng Jia
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Shiwang Huang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Chong Shen
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Hongjun Li
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhe Zhang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Lei Wang
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Gangjian Zhao
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Zhouliang Wu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yuda Lin
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Mingze Tang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Huifen Yang
- Department of Infectious Diseases, The Second Hospital of Tianjin Medical University, Tianjin, China
- *Correspondence: Huifen Yang, ; Hailong Hu,
| | - Hailong Hu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Key Laboratory of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- *Correspondence: Huifen Yang, ; Hailong Hu,
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