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Ramachandran K, Sethuraman N, Yuvaraj G, Chokkalingam V. Mycoplasma salivarium in a Retropharyngeal abscess - nidus in a niche! Diagn Microbiol Infect Dis 2024; 110:116416. [PMID: 38943820 DOI: 10.1016/j.diagmicrobio.2024.116416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Retropharyngeal abscess (RPA) is considered one of the life threatening conditions which can present either as dysphagia or dyspnoea. Timely management for the airway obstruction along with etiology identification plays a pivotal role in saving a patient's life. Here we present a case of RPA due to a rare pathogen.
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Affiliation(s)
- Krithiga Ramachandran
- Department of Microbiology, Apollo Main Hospital, Greams Road, Chennai 600006, India
| | - Nandini Sethuraman
- Department of Microbiology, Apollo Main Hospital, Greams Road, Chennai 600006, India.
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Gaillard T, Dupieux-Chabert C, Roux AL, Tessier E, Boutet-Dubois A, Courboulès C, Corvec S, Bémer P, Lavigne JP, El Sayed F, Marchandin H, Munier C, Chanard E, Gazzano V, Loiez C, Laurent F. A prospective multicentre evaluation of BioFire® Joint Infection Panel for the rapid microbiological documentation of acute arthritis. Clin Microbiol Infect 2024; 30:905-910. [PMID: 38522842 DOI: 10.1016/j.cmi.2024.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
OBJECTIVES To assess the performance of the rapid syndromic BioFire® Joint Infection Panel (BF-JIP) to detect bacterial and fungal pathogens, as well as antibiotic resistance genes, directly in synovial fluid specimens collected from patients with acute arthritis. METHODS The study was conducted in six French bacteriological laboratories. To assess the performances of BF-JIP, results were compared with those of synovial fluid 14-day culture and, in case of discrepancy, with those of complementary molecular methods and intraoperative samples. A total of 308 synovial fluid specimens were tested after collection from 308 adults and children presenting with clinical and biological suspicion of acute arthritis; patients presenting with acute periprosthetic joint infection were included according to the European Bone and Joint Infection Society 2021 criteria. RESULTS Only one specimen failed (no result). On the basis of the consolidated data, the BF-JIP was concordant with the 14-day culture in 280 (91.2%) of the 307 specimens finally included in the study. The positive percentage agreement was 84.9% (95% CI, 78.8-89.8%) and the negative percentage agreement was 100% (95% CI, 97.2-100%). The positive predictive value was extremely high (100%; 95% CI, 97.6-100%), whereas the negative predictive value was lower (82.6%; 95% CI, 75.7-88.2%), partially explained by the missing target species in the panel. DISCUSSION The BF-JIP showed high performances to detect pathogens involved in acute arthritis.
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Affiliation(s)
- Tiphaine Gaillard
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Hôpital Croix-Rousse, Lyon, France.
| | - Céline Dupieux-Chabert
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Hôpital Croix-Rousse, Lyon, France
| | - Anne-Laure Roux
- Département de Microbiologie, Ambroise Paré University Hospital, Boulogne-Billancourt, France
| | - Eve Tessier
- Département de Bactériologie, Centre Hospitalo-Universitaire de Nantes, Nantes, France
| | - Adeline Boutet-Dubois
- Département de Microbiologie et d'hygiène Hospitalière, Centre Hospitalo-Universitaire de Nîmes, Nîmes, France
| | - Camille Courboulès
- Département de Microbiologie, Ambroise Paré University Hospital, Boulogne-Billancourt, France
| | - Stéphane Corvec
- Département de Bactériologie, Centre Hospitalo-Universitaire de Nantes, Nantes, France
| | - Pascale Bémer
- Département de Bactériologie, Centre Hospitalo-Universitaire de Nantes, Nantes, France
| | - Jean-Philippe Lavigne
- Département de Microbiologie et d'hygiène Hospitalière, Centre Hospitalo-Universitaire de Nîmes, Nîmes, France
| | - Faten El Sayed
- Département de Microbiologie, Ambroise Paré University Hospital, Boulogne-Billancourt, France
| | - Hélène Marchandin
- Département de Microbiologie et d'hygiène Hospitalière, Centre Hospitalo-Universitaire de Nîmes, Nîmes, France
| | - Clément Munier
- Département de Microbiologie, Cerballiance Rhône-Alpes, Lyon, France
| | - Emmanuel Chanard
- Département de Microbiologie, Cerballiance Rhône-Alpes, Lyon, France
| | - Vincent Gazzano
- Département de Microbiologie, Cerballiance Rhône-Alpes, Lyon, France
| | - Caroline Loiez
- Centre Hospitalo-Universitaire de Lille, Institut de Microbiologie - Centre de Biologie Pathologie, Service Bactériologie, Lille, France
| | - Frédéric Laurent
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de Bactériologie, Hôpital Croix-Rousse, Lyon, France
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Jang WS, Park S, Bae JH, Yoon SY, Lim CS, Cho MC. Development of a multiplex Loop-Mediated Isothermal Amplification (LAMP) for the diagnosis of bacterial periprosthetic joint infection. PLoS One 2024; 19:e0302783. [PMID: 38753660 PMCID: PMC11098349 DOI: 10.1371/journal.pone.0302783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Periprosthetic joint infection (PJI) is one of the most serious and debilitating complications that can occur after total joint arthroplasty. Therefore, early diagnosis and appropriate treatment are important for a good prognosis. Recently, molecular diagnostic methods have been widely used to detect the causative microorganisms of PJI sensitively and rapidly. The Multiplex Loop-Mediated Isothermal Amplification (LAMP) method eliminates the complex temperature cycling and delays caused by temperature transitions seen in polymerase chain reaction (PCR) methods, making it faster and easier to perform compared to PCR-based assays. Therefore, this study developed a multiplex LAMP assay for diagnosing bacterial PJI using LAMP technology and evaluated its analytical and clinical performance. METHODS We developed a multiplex LAMP assay for the detection of five bacteria: Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus agalactiae, Pseudomonas aeruginosa, and Escherichia coli, frequently observed to be the causative agents of PJI. The method of analytical sensitivity and cross-reactivity were determined by spiking standard strains into the joint synovial fluid. The analytical sensitivity of the multiplex LAMP assay was compared with that of a quantitative real-time PCR (qPCR) assay. Clinical performance was evaluated using 20 joint synovial fluid samples collected from patients suspected of having bacterial PJI. RESULTS The analytical sensitivity of the gram-positive bacterial multiplex LAMP assay and qPCR were 105/104 CFU/mL, 103/103 CFU/mL, and 105/104 CFU/mL against S. agalactiae, S. epidermidis, and S. aureus, respectively. For P. aeruginosa and E. coli, the analytical sensitivity of the multiplex LAMP and qPCR assays were 105/104 and 106/104 CFU/mL, respectively. The multiplex LAMP assay detects target bacteria without cross-reacting with other bacteria, and exhibited 100% sensitivity and specificity in clinical performance evaluation. CONCLUSIONS This multiplex LAMP assay can rapidly detect five high-prevalence bacterial species causing bacterial PJI, with excellent sensitivity and specificity, in less than 1 h, and it may be useful for the early diagnosis of PJI.
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Affiliation(s)
- Woong Sik Jang
- Department of Emergency Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seoyeon Park
- Department of Laboratory Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ji Hoon Bae
- Department of Orthopaedic Surgery, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Young Yoon
- Department of Laboratory Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Min-Chul Cho
- Department of Laboratory Medicine, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Republic of Korea
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Hernández-Castro C, Múnera Duque A, Hoyos Burgos JP, Toro Londoño MÁ, Agudelo López SDP, Carmena D, Sánchez S. Draft genome sequences of four Morganella morganii strains isolated from Colombian colorectal cancer patient stool specimens. Microbiol Resour Announc 2024; 13:e0107723. [PMID: 38265220 PMCID: PMC10868278 DOI: 10.1128/mra.01077-23] [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: 11/13/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
We report the draft genome sequences of four Morganella morganii strains isolated from the stools of four patients diagnosed with colorectal cancer (CRC) in Medellín, Colombia. These genomes represent an important addition to the limited number of genomes of M. morganii strains originating from CRC patients currently available.
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Affiliation(s)
- Carolina Hernández-Castro
- Parasitology Group, Faculty of Medicine, Academic Corporation for the Study of Tropical Pathologies, University of Antioquia, Medellín, Colombia
- Reference and Research Laboratory on Parasitology, Spanish National Centre for Microbiology, Health Institute Carlos III, Madrid, Spain
| | - Alejandro Múnera Duque
- Department of Surgery, Faculty of Medicine, University of Antioquia, Medellín, Colombia
- Hospital Alma Máter de Antioquia, Medellín, Colombia
| | | | - Miguel Ángel Toro Londoño
- Parasitology Group, Faculty of Medicine, Academic Corporation for the Study of Tropical Pathologies, University of Antioquia, Medellín, Colombia
| | - Sonia del Pilar Agudelo López
- Parasitology Group, Faculty of Medicine, Academic Corporation for the Study of Tropical Pathologies, University of Antioquia, Medellín, Colombia
| | - David Carmena
- Reference and Research Laboratory on Parasitology, Spanish National Centre for Microbiology, Health Institute Carlos III, Madrid, Spain
- CIBERINFEC, ISCIII - CIBER Infectious Diseases, Health Institute Carlos III, Madrid, Spain
| | - Sergio Sánchez
- Reference and Research Laboratory on Food and Waterborne Bacterial Infections, Spanish National Centre for Microbiology, Health Institute Carlos III, Madrid, Spain
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Ramos MT, Chang G, Wilson C, Gilbertie J, Krieg J, Parvizi J, Chen AF, Otto CM, Schaer TP. Dogs can detect an odor profile associated with Staphylococcus aureus biofilms in cultures and biological samples. FRONTIERS IN ALLERGY 2024; 5:1275397. [PMID: 38414670 PMCID: PMC10896932 DOI: 10.3389/falgy.2024.1275397] [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: 08/09/2023] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
Introduction The study investigated the utilization of odor detection dogs to identify the odor profile of Staphylococcus aureus (S. aureus) biofilms in pure in vitro samples and in in vivo biosamples from animals and humans with S. aureus periprosthetic joint infection (PJI). Biofilms form when bacterial communities aggregate on orthopedic implants leading to recalcitrant infections that are difficult to treat. Identifying PJI biofilm infections is challenging, and traditional microbiological cultures may yield negative results even in the presence of clinical signs. Methods Dogs were trained on pure in vitro S. aureus biofilms and tested on lacrimal fluid samples from an in vivo animal model (rabbits) and human patients with confirmed S. aureus PJI. Results The results demonstrated that dogs achieved a high degree of sensitivity and specificity in detecting the odor profile associated with S. aureus biofilms in rabbit samples. Preliminary results suggest that dogs can recognize S. aureus volatile organic compounds (VOCs) in human lacrimal fluid samples. Discussion Training odor detection dogs on in vitro S. aureus, may provide an alternative to obtaining clinical samples for training and mitigates biosecurity hazards. The findings hold promise for culture-independent diagnostics, enabling early disease detection, and improved antimicrobial stewardship. In conclusion, this research demonstrates that dogs trained on in vitro S. aureus samples can identify the consistent VOC profile of PJI S. aureus biofilm infections. The study opens avenues for further investigations into a retained VOC profile of S. aureus biofilm infection. These advancements could revolutionize infectious disease diagnosis and treatment, leading to better patient outcomes and addressing the global challenge of antimicrobial resistance.
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Affiliation(s)
- Meghan T Ramos
- Penn Vet Working Dog Center, Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Gerard Chang
- Department of Orthopaedics, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
| | - Clara Wilson
- Penn Vet Working Dog Center, Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jessica Gilbertie
- Center for One Health Research Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States
| | - James Krieg
- Rothman Orthopaedic Institute, Philadelphia, PA, United States
| | - Javad Parvizi
- Rothman Orthopaedic Institute, Philadelphia, PA, United States
| | - Antonia F Chen
- Department of Orthopaedics, Harvard Medical School, Brigham and Women's Hospital, Harvard University, Boston, MA, United States
| | - Cynthia M Otto
- Penn Vet Working Dog Center, Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Thomas P Schaer
- Department of Clinical Studies New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA, United States
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Offerhaus C, Leutheuser S, Jaecker V, Shafizadeh S, Bardtke L, Wisplinghoff H, Jazmati N. Evidence of Bacterial Metabolism in Synovial Fluid of Patients With Graft Failure After Anterior Cruciate Ligament Reconstruction: A Microbiological Comparison of Primary Anterior Cruciate Ligament and Hamstring Tendon Autograft Ruptures. Arthroscopy 2024; 40:400-408. [PMID: 37437788 DOI: 10.1016/j.arthro.2023.06.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/14/2023]
Abstract
PURPOSE To investigate whether the bacterial presence in a primary ruptured native anterior cruciate ligament (ACL) differs from that in a ruptured hamstrings ACL autograft and whether low-grade infections cumulatively can be detected in the case of graft failure. METHODS In a retrospective case-control study with prospectively collected data, synovial fluid aspirates and tissue samples of failed ACL grafts were examined for evidence of bacterial colonization and compared to samples of the native ACL in primary ACL reconstruction (ACLR) using microbiological culture, 16S rRNA-PCR and histopathological examination. Furthermore, synovial fluid aspiration was investigated for possible future biomarkers for a low-grade infection. RESULTS A total of 112 consecutive patients undergoing primary ACLR without history of previous surgeries to the affected knee (n = 59) and revision ACLR after reconstruction with a hamstring tendon autograft (n = 53) were recruited from one center. No patient had a history or showed clinical signs of infection. A total of 389 samples were analyzed by culture. Bacteria were detected in 9.4% of patients with a graft rupture (n = 5/53) compared to 3.4% of patients with a primary ACL rupture (n = 2/59) showing no statistical difference (P = .192). One patient with a "true" low-grade infection was found in our study population, resulting in a prevalence of 1.9% (1/53) in the graft group. The percentage of polymorphonuclear leukocytes (PMN%) as a highly sensitive marker for joint infections was significantly higher in aspirated synovial fluid of graft ruptures (27% ± 3% vs 20% ± 4%; P = .032), as well as glucose levels were significantly lower (83 mg/dL ± 2 mg/dL vs 88 mg/dL ± 2 mg/dL; P = .042). CONCLUSIONS Synovial fluid obtained before revision ACLR showed a higher percentage of polymorphonuclear leukocytes and lower glucose levels compared with primary ACLR, suggesting bacterial metabolism and demonstrating that the intra-articular milieu changes significantly after ACLR. Tissue samples of ACL grafts revealed a low-grade infection in one case, although overall cultivable bacterial presence did not differ significantly when compared to samples of a native ACL. LEVEL OF EVIDENCE Level III, retrospective case-control study.
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Affiliation(s)
- Christoph Offerhaus
- Department of Orthopedic Surgery and Sports Traumatology, Witten/Herdecke University, Sana Medical Centre, Cologne, Germany.
| | - Sebastian Leutheuser
- Department of Orthopedic Surgery and Sports Traumatology, Witten/Herdecke University, Sana Medical Centre, Cologne, Germany
| | - Vera Jaecker
- Department of Trauma Surgery, Orthopaedic Surgery and Sports Traumatology, Witten/Herdecke University, Cologne Merheim Medical Centre, Cologne, Germany
| | - Sven Shafizadeh
- Department of Orthopedic Surgery and Sports Traumatology, Witten/Herdecke University, Sana Medical Centre, Cologne, Germany
| | | | - Hilmar Wisplinghoff
- Labor Dr. Wisplinghoff, Cologne, Germany; Institute for Virology and Microbiology, Witten/Herdecke University, Witten, Germany
| | - Nathalie Jazmati
- Labor Dr. Wisplinghoff, Cologne, Germany; Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
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Lewinski MA, Alby K, Babady NE, Butler-Wu SM, Bard JD, Greninger AL, Hanson K, Naccache SN, Newton D, Temple-Smolkin RL, Nolte F. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 2023; 25:857-875. [PMID: 37757952 DOI: 10.1016/j.jmoldx.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.
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Affiliation(s)
- Michael A Lewinski
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Roche Molecular Systems, San Clemente, California.
| | - Kevin Alby
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - N Esther Babady
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan M Butler-Wu
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Dien Bard
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander L Greninger
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Kimberly Hanson
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah
| | - Samia N Naccache
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Microbiology, LabCorp Seattle, Seattle, Washington
| | - Duane Newton
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Bio-Rad Laboratories, Irvine, California
| | | | - Frederick Nolte
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
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Offerhaus C, Jaecker V, Shafizadeh S, Müller L, Hahne H, Wisplinghoff H, Jazmati N. Semitendinosus tendons are commonly contaminated with skin flora during graft harvest for anterior cruciate ligament reconstruction. Knee Surg Sports Traumatol Arthrosc 2023; 31:4824-4832. [PMID: 37561186 PMCID: PMC10598102 DOI: 10.1007/s00167-023-07522-9] [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: 02/11/2023] [Accepted: 07/24/2023] [Indexed: 08/11/2023]
Abstract
PURPOSE To investigate the rate of bacterial contamination of semitendinosus (ST) tendons during graft harvest in anterior cruciate ligament reconstruction (ACLR), in order to precisely specify the underlying pathogens and obtain data on their susceptibility to potential antibiotics. METHODS In a prospective study, a total of 59 consecutive patients undergoing primary ACLR were recruited from one centre. No patient had history of previous surgery to the knee or showed clinical signs of infection. Four tissue samples of harvested ST tendons for anterior cruciate ligament (ACL) autografts (case group; ST) were examined for evidence of bacterial colonisation and compared to four tissue samples of the native ACL as negative controls (control group; ACL). Three of the respective samples were subjected to cultural microbiological examination and one to 16S rRNA-PCR. Antibiotic susceptibility testing was performed for each pathogen that was identified. RESULTS A total of 342 samples were analysed by culture. Significantly more patients showed a positive culture of the ST (33.9%; n = 20/59) compared to 3.4% of patients (n = 2/59) with positive culturing of the ACL (p < 0.0001). Including 16S rRNA-PCR, in a total of 42.4% (25/59) of patients, bacteria were detected in at least one ST sample either by PCR and/or culture. All species found (n = 33) belong to the typical skin flora with Staphylococcus epidermidis (39.4%; n = 13/33) being the most common species, followed by Staphylococcus capitis (24.2%; n = 8/33). All tested isolates (n = 29) were susceptible to vancomycin (29/29, 100%), 69% (n = 20/29) to oxacillin and 65.5% (n = 19/29) to clindamycin. CONCLUSION ST autografts for ACLR were commonly contaminated with skin commensal bacteria during harvest. One-third of the isolates showed resistance to typical perioperative intravenous antibiotics, whereas all isolates were sensitive to vancomycin. Therefore, routine prophylactic decontamination of all hamstring autografts before implantation should be recommended, preferably with topical vancomycin. LEVEL OF EVIDENCE Level III.
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Affiliation(s)
- Christoph Offerhaus
- Department of Orthopedic Surgery and Sports Traumatology, Sana Medical Centre, Witten/Herdecke University, Aachener Str. 445-449, 50933, Cologne, Germany.
| | - Vera Jaecker
- Department of Trauma Surgery, Orthopaedic Surgery and Sports Traumatology, Cologne Merheim Medical Centre, Witten/Herdecke University, Cologne, Germany
- Center for Musculoskeletal Surgery, Charité - University Medicine Berlin, Berlin, Germany
| | - Sven Shafizadeh
- Department of Orthopedic Surgery and Sports Traumatology, Sana Medical Centre, Witten/Herdecke University, Aachener Str. 445-449, 50933, Cologne, Germany
| | - Leonard Müller
- Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Heiko Hahne
- Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Hilmar Wisplinghoff
- Wisplinghoff Laboratories, Cologne, Germany
- Institute for Virology and Microbiology, Witten/Herdecke University, Witten, Germany
| | - Nathalie Jazmati
- Wisplinghoff Laboratories, Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
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Richarme C, Pavese P, Rubens-Duval B, Seurat O, Le Marechal M, Boisset S. Diagnostic performances and therapeutic impact of the Unyvero Implant and Tissue Infection multiplex PCR in periprosthetic joint infections. Future Microbiol 2023; 18:723-734. [PMID: 37526180 DOI: 10.2217/fmb-2022-0245] [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: 08/02/2023] Open
Abstract
Aim: We evaluated the diagnostic performances of Unyvero Implant and Tissue Infection multiplex PCR (mPCR) (Curetis) and the clinical impact of this PCR on therapeutic decisions. Materials & methods: A mPCR was performed on 33 joint fluids in addition to standard culture. A group of experts analyzed a posteriori the impact of the mPCR in the patient management. Results: The rate of concordance with culture was 74% (20/27). The sensitivity of the PCR was 59% and the specificity 90%. Clinicians would have started an appropriate treatment sooner for six patients (from 2 to 22 days earlier). Conclusion: The PCR would improve the management of 22% of the patients. For other patients, mPCR results have to be completed with the culture.
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Affiliation(s)
- Claire Richarme
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
| | - Patricia Pavese
- Service de maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
| | - Brice Rubens-Duval
- Service de chirurgie orthopédique et de traumatologie du sport, Hôpital Sud, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
| | - Olivier Seurat
- Service de chirurgie orthopédique et traumatologique, Hôpital Nord, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
| | - Marion Le Marechal
- Service de maladies infectieuses et tropicales, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
| | - Sandrine Boisset
- Laboratoire de bactériologie-hygiène hospitalière, Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, 38043, France
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, 38044, France
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10
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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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Tsantes AG, Altsitzioglou P, Papadopoulos DV, Lorenzo D, Romanò CL, Benzakour T, Tsukamoto S, Errani C, Angelini A, Mavrogenis AF. Infections of Tumor Prostheses: An Updated Review on Risk Factors, Microbiology, Diagnosis, and Treatment Strategies. BIOLOGY 2023; 12:314. [PMID: 36829589 PMCID: PMC9953401 DOI: 10.3390/biology12020314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/01/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
Several causes contribute to the high infection rate in tumor prostheses, including extensive tissue dissection and patients' immunosuppression due to the neoplastic disease. Most of these infections develop within the first 2 years following surgery with 70% of them occurring during the first year, while they are often associated with a low pathogen burden. The pathogenesis of infections in tumor prostheses is linked to bacteria developing in biofilms. Approximately half of them are caused by Staphylococcus spp., followed by Streptococcus spp., Enterococcus spp., and Enterobacteriaceae spp., while multiple pathogens may be isolated in up to 25% of the cases, with coagulase-negative Staphylococci (CoNS) and Enterococccus spp. being the most frequent pair. Although early detection and timely management are essential for complete resolution of these challenging infections, prompt diagnosis is problematic due to the highly varying clinical symptoms and the lack of specific preoperative and intraoperative diagnostic tests. Surgical management with one- or two-stage revision surgery is the mainstay for successful eradication of these infections. The recent advances in laboratory diagnostics and the development of biofilm-resistant prostheses over the past years have been areas of great interest, as research is now focused on prevention strategies. The aim of this study is to review and consolidate the current knowledge regarding the epidemiology, risk factors, microbiology, and diagnosis of infections of tumor prostheses, and to review the current concepts for their treatment and outcomes.
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Affiliation(s)
- Andreas G. Tsantes
- Microbiology Department, “Saint Savvas” Oncology Hospital, 11522 Athens, Greece
- Laboratory of Haematology and Blood Bank Unit, “Attiko” Hospital, School of Medicine, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Pavlos Altsitzioglou
- First Department of Orthopaedics, School of Medicine, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Dimitrios V. Papadopoulos
- 2nd Academic Department of Orthopaedics, School of Medicine, National and Kapodistrian University of Athens, 14233 Athens, Greece
| | - Drago Lorenzo
- Clinical Microbiology, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | | | | | - Shinji Tsukamoto
- Department of Orthopaedic Surgery, Nara Medical University, Nara 634-8521, Japan
| | - Costantino Errani
- Department of Orthopaedic Oncology, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Andrea Angelini
- Department of Orthopaedics and Orthopaedic Oncology, University of Padova, 35122 Padova, Italy
| | - Andreas F. Mavrogenis
- First Department of Orthopaedics, School of Medicine, National and Kapodistrian University of Athens, 12462 Athens, Greece
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Molecular Diagnosis of Osteoarticular Implant-Associated Infection: Available Techniques and How We Can Use Them. PROSTHESIS 2022. [DOI: 10.3390/prosthesis5010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite recent advances during the last few years, microbiological diagnosis of prosthetic joint infections remains a challenge. Molecular biology techniques have been developed to try to overcome this problem, and recently, many of them have become available for many laboratories. Some of them, especially commercial multiplex PCR-based assays and universal 16S rDNA homemade PCR assays, are now available in many laboratories. Moreover, new technologies have appeared, especially metagenomics and next-generation sequencing. These techniques have demonstrated their potential in many studies but appear to be experimental at present. A few studies have evaluated the possible use of these methods in the clinical routine, and a review of the critical aspects for the selection of a molecular method (accuracy, complexity, cost) was performed. Finally, a proposal for a protocol that includes molecular biology techniques was made according to the literature published in this field. In conclusion, molecular biology techniques are ready to be used in the clinical routine of a microbiology laboratory, but their use must be carried out in accordance with the many special characteristics of each laboratory. In all cases, the interpretation of the results must be conducted by a multidisciplinary team with experience in the management of these patients.
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Clinical Use of a 16S Ribosomal RNA Gene-Based Sanger and/or Next Generation Sequencing Assay to Test Preoperative Synovial Fluid for Periprosthetic Joint Infection Diagnosis. mBio 2022; 13:e0132222. [PMID: 36354331 PMCID: PMC9765659 DOI: 10.1128/mbio.01322-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Preoperative pathogen identification in patients with periprosthetic joint infection (PJI) is typically limited to synovial fluid culture. Whether sequencing-based approaches are of potential use in identification of pathogens in PJI, and if so which approach is ideal, is incompletely defined. The objective of the study was to analyze the accuracy of a 16S rRNA (rRNA) gene-based PCR followed by Sanger sequencing and/or targeted metagenomic sequencing approach (tMGS) performed on synovial fluid for PJI diagnosis. A retrospective study was conducted, analyzing synovial fluids tested between August 2020 and May 2021 at a single center. Subjects with hip, knee, shoulder, and elbow arthroplasties who had synovial fluid aspirated and clinically subjected to sequence-based testing and conventional culture were studied. A total of 154 subjects were included in the study; 118 had noninfectious arthroplasty failure (NIAF), while 36 had PJI. Clinical sensitivity and specificity for diagnosis of PJI were 69% and 100%, respectively, for the sequencing-based approach and 72% and 100%, respectively, for conventional culture (P = 0.74). The combination of both tests was more sensitive (83%) than culture alone (P = 0.04). Results of sequencing-based testing led to changes in treatment in four of 36 (11%) PJI subjects. Microbial identification was achieved using Sanger and next generation sequencing in 19 and 6 subjects, respectively. When combined with culture, the described 16S rRNA gene sequencing-based approach increased sensitivity compared to culture alone, suggesting its potential use in the diagnosis of PJI when synovial fluid culture is negative. IMPORTANCE Periprosthetic joint infection (PJI) is a dreadful complication of joint replacement. Noninvasive identification of infectious pathogens has been traditionnally limited to culture-based testing of synovial fluid which has poor sensitivity. Sanger and Next-generation sequencing (NGS) may be used for synovial fluid testing in PJI, but experience in routine practice is sparse. We used a targeted metagenomic sequencing approach for routine testing of synovial fluid involving NGS when Sanger sequencing had failed or was likely to fail. The objective of this study was to analyze the approach's performance for diagnosis of PJI in comparison to culture for testing synovial fluid. Overall, the sequencing-based approach was not superior to culture for diagnosis of PJI, but yielded positive results in some culture-negative samples.
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Quirino A, Marascio N, Scarlata GGM, Cicino C, Pavia G, Pantanella M, Carlisi G, Mercurio M, Familiari F, Rotundo S, Olivadese V, La Gamba V, Serapide F, Gasparini G, Matera G. Orthopedic Device-Related Infections Due to Emerging Pathogens Diagnosed by a Combination of Microbiological Approaches: Case Series and Literature Review. Diagnostics (Basel) 2022; 12:diagnostics12123224. [PMID: 36553231 PMCID: PMC9778170 DOI: 10.3390/diagnostics12123224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Orthopedic and trauma device-related infections (ODRI) due to high virulence microorganisms are a devastating complication after orthopedic surgery. Coagulase-negative Staphylococci (CoNS) are mainly involved but commensal bacteria, located in human mucous membranes, are emerging pathogens in ODRI. Currently, bacterial culture is the gold standard for ODRI but the diagnostic process remains time consuming and laborious. We evaluated a combination of microbiological approaches in the diagnosis of emerging pathogens involved in ODRI. We analyzed two synovial fluids, five tissue samples and five surgical wound swabs from two different patients with ODRI, attending the Department of Orthopedic and Trauma Surgery of Mater Domini Teaching Hospital, Catanzaro, Italy. Identification was carried out with a combination of microbiological approaches (culture, mass spectrometry and 16s rRNA gene sequencing). We demonstrated the importance of a combination of microbiological approaches for the diagnosis of emerging pathogens in ODRI, because the low number of cases in the literature makes it very difficult to formulate guidelines for the management of patients.
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Affiliation(s)
- Angela Quirino
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Graecia” University, 88100 Catanzaro, Italy
| | - Nadia Marascio
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Graecia” University, 88100 Catanzaro, Italy
- Correspondence:
| | | | - Claudia Cicino
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Graecia” University, 88100 Catanzaro, Italy
| | - Grazia Pavia
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Graecia” University, 88100 Catanzaro, Italy
| | - Marta Pantanella
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Graecia” University, 88100 Catanzaro, Italy
| | - Giovanni Carlisi
- Unit of Orthopedic and Trauma Surgery, Department of Medical and Surgical Sciences, “Magna Græcia” University, 88100 Catanzaro, Italy
| | - Michele Mercurio
- Unit of Orthopedic and Trauma Surgery, Department of Medical and Surgical Sciences, “Magna Græcia” University, 88100 Catanzaro, Italy
| | - Filippo Familiari
- Unit of Orthopedic and Trauma Surgery, Department of Medical and Surgical Sciences, “Magna Græcia” University, 88100 Catanzaro, Italy
| | - Salvatore Rotundo
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, “Magna Graecia” University, 88100 Catanzaro, Italy
| | - Vincenzo Olivadese
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, “Magna Graecia” University, 88100 Catanzaro, Italy
| | - Valentina La Gamba
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, “Magna Graecia” University, 88100 Catanzaro, Italy
| | - Francesca Serapide
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, “Magna Graecia” University, 88100 Catanzaro, Italy
| | - Giorgio Gasparini
- Unit of Orthopedic and Trauma Surgery, Department of Medical and Surgical Sciences, “Magna Græcia” University, 88100 Catanzaro, Italy
| | - Giovanni Matera
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Graecia” University, 88100 Catanzaro, Italy
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Han HS, Ro DH, Chung J, Kim N, Moon J. Nanopore 16S amplicon sequencing enables rapid detection of pathogen in knee periprosthetic joint infection. Int J Med Microbiol 2022; 312:151570. [PMID: 36288682 DOI: 10.1016/j.ijmm.2022.151570] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/06/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES We investigated whether nanopore 16S amplicon sequencing is capable of bacterial identification in patients with knee prosthetic joint infection (PJI), and we compared its efficacy with conventional culture studies. METHODS In total, 36 patients who had clinical manifestation suspected of PJI were enrolled in this study. To begin, synovial fluids were aspirated from the affected knee using aseptic technique and tissues specimens were obtained during the surgery. Next, DNA was extracted from the synovial fluid or tissues, and 16S rDNA PCR was performed. In PCR positive cases, nanopore amplicon sequencing was then performed for up to 3 h. The results of amplicon sequencing were compared to those of conventional culture studies. RESULTS Of the 36 patients enrolled, 22 were classified as true infections according to the MSIS criteria whereas 14 were considered uninfected. Among the 22 PJI cases, 19 cases were culture positive (CP-PJI) while three cases were culture negative (CN-PJI). In 14 of 19 (73.7 %) CP- PJI cases, 16S sequencing identified concordant bacteria with conventional culture studies with a significantly shorter turnaround time. In some cases, nanopore 16S sequencing was superior to culture studies in the species-level identification of pathogen and detection of polymicrobial infections. Altogether, in the majority of PJI candidate patients (32 of 36, 88.9 %), 16S sequencing achieved identical results to cultures studies with a significantly reduced turnaround time (100.9 ± 32.5 h vs. 10.8 ± 7.7 h, p < 0.001). CONCLUSIONS Nanopore 16S sequencing was found to be particularly useful for pathogen identification in knee PJI. Although the sensitivity was not superior to culture studies, the nanopore 16S sequencing was much faster, and species-level identification and detection of polymicrobial infections were superior to culture studies.
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Affiliation(s)
- Hyuk-Soo Han
- Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Du Hyun Ro
- Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeehyeok Chung
- Department of Orthopaedic Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Narae Kim
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - Jangsup Moon
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea; Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea.
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Gazendam A, Wood TJ, Tushinski D, Bali K. Diagnosing Periprosthetic Joint Infection: a Scoping Review. Curr Rev Musculoskelet Med 2022; 15:219-229. [PMID: 35368214 PMCID: PMC9107560 DOI: 10.1007/s12178-022-09751-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/15/2022] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW The goal of this review is to provide an up to date understanding of the utility and limitations of the current tests utilized in the diagnosis of periprosthetic joint infection (PJI) in total knee and hip arthroplasty. RECENT FINDINGS Despite the growth in literature surrounding PJI diagnosis, there remains challenges in establishing a diagnosis of PJI. A combination of clinical, serum, and synovial tests and microbiologic and histologic examinations can yield a diagnosis in the majority of cases. Novel molecular and imaging studies may be beneficial for indeterminant cases. A number of emerging diagnostic tests have been proposed and may be incorporated into diagnostic algorithms in the future. Recently proposed stepwise diagnostic algorithms have shown high sensitivity and specificity. The diagnosis of PJI remains challenging due to a lack of tests that can definitively rule out infection. Diagnosis and investigations should occur in a stepwise fashion. There has been a plethora of new diagnostic tests introduced in attempts to improve the accuracy of diagnostic algorithms. The definition and algorithms for the diagnoses of PJI will continue to evolve as new techniques and tests are introduced.
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Affiliation(s)
- Aaron Gazendam
- Department of Surgery, Division of Orthopaedic Surgery, McMaster University, Hamilton, Ontario, Canada
| | - Thomas J Wood
- Department of Surgery, Division of Orthopaedic Surgery, McMaster University, Hamilton, Ontario, Canada
| | - Daniel Tushinski
- Department of Surgery, Division of Orthopaedic Surgery, McMaster University, Hamilton, Ontario, Canada
| | - Kamal Bali
- Department of Surgery, Division of Orthopaedic Surgery, McMaster University, Hamilton, Ontario, Canada.
- Juravinski Hospital, 711 Concession St, Hamilton, Ontario, L8V 1C3, Canada.
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Fast and Sensitive Multiplex Real-Time Quantitative PCR to Detect Cutibacterium Periprosthetic Joint Infections. J Mol Diagn 2022; 24:666-673. [PMID: 35364323 DOI: 10.1016/j.jmoldx.2022.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/31/2022] [Accepted: 03/04/2022] [Indexed: 12/26/2022] Open
Abstract
Diagnosis of Cutibacterium periprosthetic joint infections (PJIs) is challenging due to a long cultivation time of up to 14 days. Faster culture-independent diagnosis would improve patient care with early and accurate treatment. Specific primers and probes were designed for Cutibacterium acnes, Cutibacterium avidum, and Cutibacterium granulosum and evaluated in a multiplex TaqMan real-time quantitative PCR (qPCR) format on 57 skin swabs and 20 culture-negative cerebrospinal fluid samples. The multiplex qPCR was tested in a PJI cohort of 41 sonication fluid samples from removed implants infected with different pathogens. All five culture-positive Cutibacterium PJIs were detected with the corresponding Cutibacterium-specific probe (100% positive percent agreement). The multiplex qPCR additionally detected C. avidum in two PJI sonication fluid samples that were diagnosed as Staphylococcus species infections according to culture (95% negative percent agreement). The new multiplex qPCR can provide a Cutibacterium PJI diagnosis within 1 day, allowing early and accurate antibiotic treatment. A prospective diagnostic trial in PJI with a high number of Cutibacterium species infections (shoulder PJI) is needed for further evaluation.
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Bernard E, Peyret T, Plinet M, Contie Y, Cazaudarré T, Rouquet Y, Bernier M, Pesant S, Fabre R, Anton A, Maugis-Rabusseau C, François JM. The DendrisCHIP ® Technology as a New, Rapid and Reliable Molecular Method for the Diagnosis of Osteoarticular Infections. Diagnostics (Basel) 2022; 12:1353. [PMID: 35741163 PMCID: PMC9222036 DOI: 10.3390/diagnostics12061353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022] Open
Abstract
Osteoarticular infections are major disabling diseases that can occur after orthopedic implant surgery in patients. The management of these infections is very complex and painful, requiring surgical intervention in combination with long-term antibiotic treatment. Therefore, early and accurate diagnosis of the causal pathogens is essential before formulating chemotherapeutic regimens. Although culture-based microbiology remains the most common diagnosis of osteoarticular infections, its regular failure to identify the causative pathogen as well as its long-term modus operandi motivates the development of rapid, accurate, and sufficiently comprehensive bacterial species-specific diagnostics that must be easy to use by routine clinical laboratories. Based on these criteria, we reported on the feasibility of our DendrisCHIP® technology using DendrisCHIP®OA as an innovative molecular diagnostic method to diagnose pathogen bacteria implicated in osteoarticular infections. This technology is based on the principle of microarrays in which the hybridization signals between oligoprobes and complementary labeled DNA fragments from isolates queries a database of hybridization signatures corresponding to a list of pre-established bacteria implicated in osteoarticular infections by a decision algorithm based on machine learning methods. In this way, this technology combines the advantages of a PCR-based method and next-generation sequencing (NGS) while reducing the limitations and constraints of the two latter technologies. On the one hand, DendrisCHIP®OA is more comprehensive than multiplex PCR tests as it is able to detect many more germs on a single sample. On the other hand, this method is not affected by the large number of nonclinically relevant bacteria or false positives that characterize NGS, as our DendrisCHIP®OA has been designed to date to target only a subset of 20 bacteria potentially responsible for osteoarticular infections. DendrisCHIP®OA has been compared with microbial culture on more than 300 isolates and a 40% discrepancy between the two methods was found, which could be due in part but not solely to the absence or poor identification of germs detected by microbial culture. We also demonstrated the reliability of our technology in correctly identifying bacteria in isolates by showing a convergence (i.e., same bacteria identified) with NGS superior to 55% while this convergence was only 32% between NGS and microbial culture data. Finally, we showed that our technology can provide a diagnostic result in less than one day (technically, 5 h), which is comparatively faster and less labor intensive than microbial cultures and NGS.
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Affiliation(s)
- Elodie Bernard
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Thomas Peyret
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Mathilde Plinet
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Yohan Contie
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Thomas Cazaudarré
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Yannick Rouquet
- Laboratoire CBM-Inovie, F-31000 Toulouse, France; (Y.R.); (M.B.); (R.F.)
| | - Matthieu Bernier
- Laboratoire CBM-Inovie, F-31000 Toulouse, France; (Y.R.); (M.B.); (R.F.)
| | - Stéphanie Pesant
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Richard Fabre
- Laboratoire CBM-Inovie, F-31000 Toulouse, France; (Y.R.); (M.B.); (R.F.)
| | - Aurore Anton
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
| | - Cathy Maugis-Rabusseau
- Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, INSA, F-31077 Toulouse, France;
| | - Jean Marie François
- Dendris SAS, 335 rue du Chêne Vert, F-31670 Labège, France; (E.B.); (T.P.); (M.P.); (Y.C.); (T.C.); (S.P.); (A.A.)
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 Avenue de Rangueil, F-31077 Toulouse, France
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Sambri A, Fiore M, Tedeschi S, De Paolis M. The Need for Multidisciplinarity in Modern Medicine: An Insight into Orthopaedic Infections. Microorganisms 2022; 10:microorganisms10040756. [PMID: 35456807 PMCID: PMC9028939 DOI: 10.3390/microorganisms10040756] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023] Open
Affiliation(s)
- Andrea Sambri
- Orthopaedics and Traumatology Department, IRCCS Azienda Ospedaliero Universitaria di Bologna, Via Massarenti 9, 40138 Bologna, Italy; (M.F.); (M.D.P.)
- Correspondence:
| | - Michele Fiore
- Orthopaedics and Traumatology Department, IRCCS Azienda Ospedaliero Universitaria di Bologna, Via Massarenti 9, 40138 Bologna, Italy; (M.F.); (M.D.P.)
| | - Sara Tedeschi
- Infectious Disease Department, IRCCS Azienda Ospedaliero Universitaria di Bologna, Via Massarenti 9, 40138 Bologna, Italy;
| | - Massimiliano De Paolis
- Orthopaedics and Traumatology Department, IRCCS Azienda Ospedaliero Universitaria di Bologna, Via Massarenti 9, 40138 Bologna, Italy; (M.F.); (M.D.P.)
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Abstract
The gold standard for confirming bacterial infections is culture-positive, which has a long sample-to-result turnaround time and poor sensitivity for unculturable and fastidious pathogens; therefore, it is hard to guide early, targeted antimicrobial therapy and reduce overuse of broad-spectrum antibiotics. Nanopore targeted sequencing (NTS) is reported to be advantageous in detection speed and range over culture in prior published reports. However, investigation of the clinical performance of NTS is deficient at present. Thus, we assessed the feasibility of NTS for the first time with cohort and systematic comparisons with traditional culture assays and PCR followed by Sanger sequencing. This retrospective study was performed on 472 samples, including 6 specimen types from 436 patients, to evaluate the clinical performance of NTS designed for identifying the microbial composition of various infections. Of these samples, 86.7% were found to be NTS positive, which was significantly higher than culture-positive (26.7%). A total of 425 significant human opportunistic bacteria and fungi detected by NTS were selected to go through validation with PCR followed by Sanger sequencing. The average accuracy rate was 85.2% (maximum 100% created by Cryptococcus neoformans, the last one 66.7% provided by both Staphylococcus haemolyticus and Moraxella osloensis, minimum 0% produced by Burkholderia cepacia). The accuracy rate also varied with sample type; the highest accuracy rate was found in pleural and ascites fluid (95.8%) followed by bronchoalveolar lavage fluid (88.7%), urine (86.8%), and wound secretions (85.0%), while the lowest was present in cerebrospinal fluid (58.8%). NTS had a diagnostic sensitivity of 94.5% and specificity of 31.8%. The positive and negative predictive values of NTS were 79.9% and 66.7%, respectively. For diagnosis of infectious diseases, the sensitivity was greatly increased by 56.7% in NTS compared with culture (94.5% vs 37.8%). Therefore, NTS can accurately detect the causative pathogens in infectious samples, particularly in pleural and ascites fluid, bronchoalveolar lavage fluid, urine, and wound secretions, with a short turnaround time of 8-14 h, and might innovatively contribute to personalizing antibiotic treatments for individuals with standardized protocols in clinical practices. IMPORTANCE Nanopore targeted sequencing (NTS) is reported to be advantageous in detection speed and range over culture in prior published reports. Investigation of the clinical performance of NTS is deficient at present. In our study, cohort and systematic comparisons among three assays (culture, NTS, and Sanger sequencing) were analyzed retrospectively for the first time. We found that NTS undoubtedly has incomparable advantages in accurately detecting the causative pathogens in infectious samples, particularly in pleural and ascites fluid, bronchoalveolar lavage fluid, urine, and wound secretions, with a short turnaround time of 8-14 h. For sterile specimens like blood and cerebrospinal fluid (CSF), the NTS outcomes should be validated using other nucleic acid based detection technology. Overall, NTS might innovatively contribute to guiding early, targeted antimicrobial therapy with lower cost and reduce overuse of broad-spectrum antibiotics.
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Berneking L, Haas M, Frielinghaus L, Berinson B, Lütgehetmann M, Christner M, Aepfelbacher M, Gerlach U, Seide K, Both A, Rohde H. Evaluation of a syndromic panel polymerase chain reaction (spPCR) assay for the diagnosis of device-associated bone and joint infections (BJI). Int J Infect Dis 2022; 116:283-288. [PMID: 35031396 DOI: 10.1016/j.ijid.2022.01.013] [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: 08/11/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVE Pathogen detection is crucial for diagnosis and targeted therapy in implant-associated bone and joint infections (BJI). Culture-based microbiology regularly fails to identify causative pathogens. This study evaluated the diagnostic accuracy and clinical usefulness of a syndromic panel polymerase chain reaction (spPCR) assay targeting common BJI pathogens in tissue specimens from patients with implant-associated BJI. METHODS Results obtained by spPCR assay and a 16S rDNA PCR were compared with results obtained from a standard of care (SOC) culture-based diagnostics, serving as a gold standard. In total, 126 specimens obtained from 73 patients were analyzed. RESULTS The spPCR assay correctly identified 33/40 culture-positive samples (82.5 %) and was positive in 9/86 (10.5 %) culture-negative samples, resulting in an overall sensitivity of 84.6 % (95% confidence interval [CI] 68.79-93.59%) and specificity of 89.35% (95% CI 80.6-94.81%). The spPCR was more sensitive compared with the 16S rDNA PCR (37.5%). The spPCR identified pathogens in 7/51 (13.7%) SOC-negative patients. Re-evaluation of spPCR results in clinical context suggested their clinical significance. CONCLUSION An spPCR assay targeting common pathogens causing implant-associated BJI may help to identify causative agents in culture-negative cases. As false-negative results are possible, spPCR assays appear as an add-on approach for pathogen detection in implant-associated BJI.
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Affiliation(s)
- Laura Berneking
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Michaela Haas
- Septische Unfallchirurgie und Orthopädie, BG Klinikum Hamburg, Hamburg, Germany
| | - Lisa Frielinghaus
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Berinson
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Lütgehetmann
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Christner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Ulf Gerlach
- Septische Unfallchirurgie und Orthopädie, BG Klinikum Hamburg, Hamburg, Germany
| | - Klaus Seide
- Septische Unfallchirurgie und Orthopädie, BG Klinikum Hamburg, Hamburg, Germany
| | - Anna Both
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.
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22
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Chisari E, Lin F, Fei J, Parvizi J. Fungal periprosthetic joint infection: Rare but challenging problem. Chin J Traumatol 2022; 25:63-66. [PMID: 35031203 PMCID: PMC9039431 DOI: 10.1016/j.cjtee.2021.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/27/2021] [Accepted: 12/03/2021] [Indexed: 02/04/2023] Open
Abstract
Periprosthetic joint infection (PJI) is the most difficult complication following total joint arthroplasty. Most of the etiological strains, accounting for over 98% of PJI, are bacterial species, with Staphylococcusaureus and Coagulase-negative staphylococci present in between 50% and 60% of all PJIs. Fungi, though rare, can also cause PJI in 1%-2% of cases and can be challenging to manage. The management of this uncommon but complex condition is challenging due to the absence of a consistent algorithm. Diagnosis of fungal PJI is difficult as isolation of the organisms by traditional culture may take a long time, and some of the culture-negative PJI can be caused by fungal organisms. In recent years, the introduction of next-generation sequencing has provided opportunity for isolation of the infective organisms in culture-negative PJI cases. The suggested treatment is based on consensus and includes operative and non-operative measures. Two-stage revision surgery is the most reliable surgical option for chronic PJI caused by fungi. Pharmacological therapy with antifungal agents is required for a long period of time with antibiotics and included to cover superinfections with bacterial species. The aim of this review article is to report the most up-to-date information on the diagnosis and treatment of fungal PJI with the intention of providing clear guidance to clinicians, researchers and surgeons.
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Affiliation(s)
- Emanuele Chisari
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Feitai Lin
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Jun Fei
- Department of Emergency Medicine of Army Medical Center, Army Medical University, Chongqing, 400042, China,State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, 400042, China
| | - Javad Parvizi
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA, 19107, USA,Corresponding author.
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23
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Goswami K, Tipton C, Clarkson S, Chang G, Tan TL, Fram B, Chisari E, Sobol K, Natoli RM, Conway JD, Altman GT, Parvizi J, Krieg JC. Fracture-Associated Microbiome and Persistent Nonunion: Next-Generation Sequencing Reveals New Findings. J Orthop Trauma 2022; 36:S40-S46. [PMID: 35061650 DOI: 10.1097/bot.0000000000002305] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2021] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Fracture nonunion remains a devastating complication and may occur for several reasons, though the microbial contribution remains poorly estimated. Next-generation sequencing (NGS) techniques, including 16S rRNA gene profiling, are capable of rapid bacterial detection within clinical specimens. Nonunion cases may harbor microbes that escape detection by conventional culture methods that contribute to persistence. Our aim was to investigate the application of NGS pathogen detection to nonunion diagnosis. METHODS In this prospective multicenter study, samples were collected from 54 patients undergoing open surgical intervention for preexisting long-bone nonunion (n = 37) and control patients undergoing fixation of an acute fracture (n = 17). Intraoperative specimens were sent for dual culture and 16S rRNA gene-based microbial profiling. Patients were followed for evidence of fracture healing, whereas patients not healed at follow-up were considered persistent nonunion. Comparative analyses aimed to determine whether microbial NGS diagnostics could discriminate between nounions that healed during follow-up versus persistent nonunion. RESULTS Positive NGS detection was significantly correlated with persistent nonunion, positive in 77% more cases than traditional culture. Nonunion cases were observed to have significantly increased diversity and altered bacterial profiles from control cases. DISCUSSION NGS seems to be a useful adjunct in identification of organisms that may contribute to nonunion. Our findings suggest that the fracture-associated microbiome may be a significant risk factor for persistent nonunion. Ongoing work aims to determine the clinical implications of isolated organisms detected by sequencing and to identify robust microbial predictors of nonunion outcomes. LEVEL OF EVIDENCE Diagnostic Level II. See Instructions for Authors for a complete description of levels of evidence.
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Affiliation(s)
- Karan Goswami
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA
| | - Craig Tipton
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
- RTL Genomics, MicroGenDX, Lubbock, TX
| | - Samuel Clarkson
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA
| | - Gerard Chang
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA
| | - Timothy L Tan
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA
| | - Brianna Fram
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA
| | - Emanuele Chisari
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA
| | - Keenan Sobol
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA
| | - Roman M Natoli
- Department of Orthopaedic Surgery, Indiana University School of Medicine, Indianapolis, IN
| | - Janet D Conway
- International Center for Limb Lengthening, Rubin Institute for Advanced Orthopedics, Sinai Hospital of Baltimore, Baltimore, MD; and
| | - Gregory T Altman
- Department of Orthopaedic Surgery, Allegheny Health Network, Pittsburgh, PA
| | - Javad Parvizi
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA
| | - James C Krieg
- Rothman Orthopaedic Institute at Thomas Jefferson University, Philadelphia, PA
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24
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Sandiford NA, Wronka K. The multidisciplinary approach to managing prosthetic joint infection: could this lead to improved outcomes? ANNALS OF JOINT 2022; 7:8. [PMID: 38529134 PMCID: PMC10929312 DOI: 10.21037/aoj-2020-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/11/2020] [Indexed: 03/27/2024]
Abstract
Periprosthetic joint infection (PJI) is a devastating complication of the total joint arthroplasty (TJA). It presents a great challenge for the treating clinician. Diagnosis as well as management can prove difficult with significant morbidity for the patients and cost for patients, health care providers and society as a whole. Outcomes of equally challenging pathology such as tumors and polytrauma have been shown to be improved when patients are managed by a team as specialists as opposed to single individuals. The purpose of this study is to review the role of the multi-disciplinary team (MDT) approach in the diagnosis and management of PJI. We examine the influence of this approach on clinical outcomes in patients with PJI. We also discuss the organisational and logistical issues associated with establishment of a MDT as well as several other issues not mentioned in the contemporary orthopaedic literature. All published literature examining the role of multidisciplinary care in the management of PJI and the influence of this approach to the management and outcomes of patients with this diagnosis were included. Studies published in languages other than English were excluded. There is a paucity of data on the influence of multidisciplinary care on outcomes of the management of PJI. Evidence suggests that the MDT has important role in ensuring all factors in the management of this complex group are considered and best possible care is delivered. Multicentre randomised clinical trials are required to assess the influence of MDT'S on outcome as well as important questions around the structuring of these teams.
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Affiliation(s)
| | - Konrad Wronka
- Department of Orthopaedic Surgery, West Suffolk Hospital, Bury St Edmonds, UK
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25
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Carr C, Wilcox H, Burton JP, Menon S, Al KF, O’Gorman D, Lanting BA, Vasarhelyi EM, Neufeld M, Teeter MG. Deciphering the low abundance microbiota of presumed aseptic hip and knee implants. PLoS One 2021; 16:e0257471. [PMID: 34520499 PMCID: PMC8439452 DOI: 10.1371/journal.pone.0257471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/01/2021] [Indexed: 11/18/2022] Open
Abstract
16S rRNA gene sequencing of DNA extracted from clinically uninfected hip and knee implant samples has revealed polymicrobial populations. However, previous studies assessed 16S rRNA gene sequencing as a technique for the diagnosis of periprosthetic joint infections, leaving the microbiota of presumed aseptic hip and knee implants largely unstudied. These communities of microorganisms might play important roles in aspects of host health, such as aseptic loosening. Therefore, this study sought to characterize the bacterial composition of presumed aseptic joint implant microbiota using next generation 16S rRNA gene sequencing, and it evaluated this method for future investigations. 248 samples were collected from implants of 41 patients undergoing total hip or knee arthroplasty revision for presumed aseptic failure. DNA was extracted using two methodologies-one optimized for high throughput and the other for human samples-and amplicons of the V4 region of the 16S rRNA gene were sequenced. Sequencing data were analyzed and compared with ancillary specific PCR and microbiological culture. Computational tools (SourceTracker and decontam) were used to detect and compensate for environmental and processing contaminants. Microbial diversity of patient samples was higher than that of open-air controls and differentially abundant taxa were detected between these conditions, possibly reflecting a true microbiota that is present in clinically uninfected joint implants. However, positive control-associated artifacts and DNA extraction methodology significantly affected sequencing results. As well, sequencing failed to identify Cutibacterium acnes in most culture- and PCR-positive samples. These challenges limited characterization of bacteria in presumed aseptic implants, but genera were identified for further investigation. In all, we provide further support for the hypothesis that there is likely a microbiota present in clinically uninfected joint implants, and we show that methods other than 16S rRNA gene sequencing may be ideal for its characterization. This work has illuminated the importance of further study of microbiota of clinically uninfected joint implants with novel molecular and computational tools to further eliminate contaminants and artifacts that arise in low bacterial abundance samples.
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MESH Headings
- Adult
- Aged
- Arthroplasty, Replacement, Hip
- Arthroplasty, Replacement, Knee
- Artifacts
- Bacteria/genetics
- Bacteria/isolation & purification
- Female
- Hip Joint/microbiology
- Humans
- Knee Joint/microbiology
- Male
- Microbiota
- Middle Aged
- Polymerase Chain Reaction
- Prosthesis-Related Infections/microbiology
- Prosthesis-Related Infections/pathology
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Charles Carr
- Canadian Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, Ontario, Canada
| | - Hannah Wilcox
- Canadian Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, Ontario, Canada
| | - Jeremy P. Burton
- Canadian Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, Ontario, Canada
- Department of Surgery, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Sharanya Menon
- Canadian Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, Ontario, Canada
| | - Kait F. Al
- Canadian Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, Ontario, Canada
| | - David O’Gorman
- Department of Surgery, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Brent A. Lanting
- Department of Surgery, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Edward M. Vasarhelyi
- Department of Surgery, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Michael Neufeld
- Department of Surgery, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Department of Orthopaedics, Adult Hip and Knee Reconstruction Service, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew G. Teeter
- Department of Surgery, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- Department of Medical Biophysics, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
- * E-mail:
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26
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Fida M, Khalil S, Abu Saleh O, Challener DW, Sohail MR, Yang JN, Pritt BS, Schuetz AN, Patel R. Diagnostic Value of 16S Ribosomal RNA Gene Polymerase Chain Reaction/Sanger Sequencing in Clinical Practice. Clin Infect Dis 2021; 73:961-968. [PMID: 34407178 DOI: 10.1093/cid/ciab167] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Accurate microbiologic diagnosis is important for appropriate management of infectious diseases. Sequencing-based molecular diagnostics are increasingly used for precision diagnosis of infections. However, their clinical utility is unclear. METHODS We conducted a retrospective analysis of specimens that underwent 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) followed by Sanger sequencing at our institution from April 2017 through March 2019. RESULTS A total of 566 specimens obtained from 460 patients were studied. Patients were considered clinically infected or noninfected based on final diagnosis and management. In 17% of patients, 16S rRNA PCR/sequencing was positive and in 5% of patients, this test led to an impact on clinical care. In comparison, bacterial cultures were positive in 21% of patients. Specimens with a positive Gram stain had 12 times greater odds of having a positive molecular result than those with a negative Gram stain (95% confidence interval for odds ratio, 5.2-31.4). Overall, PCR positivity was higher in cardiovascular specimens (37%) obtained from clinically infected patients, with bacterial cultures being more likely to be positive for musculoskeletal specimens (P < .001). 16S rRNA PCR/sequencing identified a probable pathogen in 10% culture-negative specimens. CONCLUSION 16S rRNA PCR/sequencing can play a role in the diagnostic evaluation of patients with culture-negative infections, especially those with cardiovascular infections.
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Affiliation(s)
- Madiha Fida
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarwat Khalil
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Infectious Disease and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Omar Abu Saleh
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Douglas W Challener
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Muhammad Rizwan Sohail
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Infectious Disease, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Joshua N Yang
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S Pritt
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Audrey N Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Infectious Diseases, 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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27
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Amiri S, Mohammadi Zeydi M, Amiri N. Bacillus cereus saba.zh, a novel bacterial strain for the production of bioplastic (polyhydroxybutyrate). Braz J Microbiol 2021; 52:2117-2128. [PMID: 34510397 DOI: 10.1007/s42770-021-00599-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/19/2021] [Indexed: 11/26/2022] Open
Abstract
The identification of novel bacterial strains with a high production potential of polyhydroxybutyrate (PHB) to substitute the bioplastics with non-biodegradable plastics and reducing environmental pollution is really effective. The present study was done with the purpose of PHB bioplastic production using a novel bacterial strain. Twenty-one different bacterial isolates were obtained from petrochemical wastewater, which among them, 10 isolates were PHB positive. The presence of PHB granules was detected in the isolates using Sudan Black B staining. The most excellent PHB-accumulating bacterium with a maximum yield of PHB (61.53%) was selected and identified as Bacillus cereus saba.zh, based on morphological, biochemical, and molecular techniques. 16S rRNA nucleotide sequence of the bacterium was assigned accession number: MT975245 in the NCBI database. The phylogenetic tree data showed that the closest type strain to the Bacillus cereus saba.zh is the Bacillus cereus SDB4 (91%). The three genes (phaA, phaB, and phaC) responsible for the PHB biosynthesis were amplified using the specific oligonucleotide primers by PCR technique. The highest PHB yield was achieved when the culture medium was supplemented with 3% sugarcane molasses as a carbon source, ammonium sulfate as the nitrogen source, at pH 7, and temperature of 30 °C. The characterization of the extracted polymer by FTIR and 1H NMR spectroscopy proves the presence of methyl, methylene, methine, hydroxyl, and ester carbonyl groups and confirmed the structure of biopolymer as PHB. The novel strain Bacillus cereus saba.zh has good potential as an appropriate candidate for low-cost industrial production of bioplastic.
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Affiliation(s)
- Saba Amiri
- Department of Microbiology, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran.
| | | | - Nasim Amiri
- Department of Biochemistry, Babol Branch, Islamic Azad University, Babol, Iran
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28
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Vilén A, Nilson B, Petersson AC, Cigut M, Nielsen C, Ström H. Detection of bacterial DNA in synovial fluid in dogs with arthritis: a comparison between bacterial culture and 16S rRNA polymerase chain reaction. Acta Vet Scand 2021; 63:34. [PMID: 34461947 PMCID: PMC8404341 DOI: 10.1186/s13028-021-00599-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/22/2021] [Indexed: 12/03/2022] Open
Abstract
Background Septic arthritis (SA) is a serious condition in dogs that requires a prompt diagnosis and treatment to minimize long-term joint pathology. Although bacterial detection in synovial fluid (SF) through culture or cytology is often performed to confirm diagnosis, the sensitivity of these tests is low. The need for a reliable diagnostic tool to confirm the presence of bacteria in SF in humans has led to the increased use of 16S rRNA (i.e., ribosomal RNA) gene sequencing by polymerase chain reaction (16S rRNA PCR). The aim of this prospective clinical study was to compare the sensitivity and specificity of 16S rRNA PCR with bacterial culture on blood agar plates after pre-incubation of SF in paediatric blood bacterial culture bottles to identify bacteria in dogs with clinical signs of SA and to investigate the usefulness of these methods as diagnostic tools. Results Ten dogs with clinical signs of SA, nine with osteoarthritis (OA, control group) and nine with clinical signs of immune-mediated polyarthritis (IMPA, second control group) were examined. Bacterial culture was positive in seven of 10 dogs with clinical SA, of which only two were positive by 16S rRNA PCR. The sensitivity of 16S rRNA PCR and bacterial culture analysis for dogs with clinical SA were 20% and 70%, respectively. All SF samples collected from control group (n = 9) and second control group (n = 14) animals were negative on culture, and 16S rRNA PCR rendered a specificity of 100%. Conclusions Our study showed a lower sensitivity of 16S rRNA PCR than bacterial culture for dogs with clinical SA. Our findings suggest that there is currently no advantage in using 16S rRNA PCR as a diagnostic tool for dogs with clinical SA. Furthermore, our study indicates that pre-incubation in paediatric blood bacterial culture bottles before bacterial cultivation on blood agar plates might enhance bacterial culture sensitivity compared to other culture methods.
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29
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Amiri Kojuri S, Issazadeh K, Heshmatipour Z, Mirpour M, Zarrabi S. Production of Bioplastic (Polyhydroxybutyrate) with Local Bacillus megaterium Isolated from Petrochemical Wastewater. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2849. [PMID: 34825017 PMCID: PMC8590724 DOI: 10.30498/ijb.2021.244756.2849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND Polyhydroxybutyrate is a biodegradable plastic produced by some bacteria and can completely be replaced with petroleum based non-degradable plastics. OBJECTIVES This study was done to isolate and identify one local strain with a high-production ability for industrial purposes. MATERIAL AND METHODS The sampling from petrochemical wastewater was done. The existence of polyhydroxybutyrate in isolates was studied with Sudan Black staining. Using the Sudan Black B plate assay method and estimating produced PHB amount, the most potent isolate was chosen. This isolate was distinguished by morphological and biochemical methods and determining 16S rRNA gene sequencing. The final confirmation of polyhydroxybutyrate synthesis was done by FTIR and 1H NMR. To increase more production of polyhydroxybutyrate, the effect of different factors including carbon, nitrogen, pH, and temperature were assessed. RESULTS Six bacterial isolates producing polyhydroxybutyrate were separated, which among them, one new strain of Bacillus megaterium named saba.zh was selected as better isolation. 16S rRNA nucleotide sequence of bacterium was assigned accession number: MN519999 in the NCBI database. The optimal conditions to increase the production of polyhydroxybutyrate, are using glucose as a carbon source, ammonium sulfate as the nitrogen source, in the condition with having pH 7 and temperature 30 °C. After optimizing, the production of PHB increased from 56.51% to 85.41%. CONCLUSIONS This research indicated that Bacillus megaterium saba.zh, due to better polymer yield, is a potent PHB producer which can be used for PHB industrial production.
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Affiliation(s)
- Saba Amiri Kojuri
- Department of Microbiology, Lahijan Branch, Islamic Azad University, Lahijan, Iran
| | - Khosro Issazadeh
- Department of Microbiology, Lahijan Branch, Islamic Azad University, Lahijan, Iran
| | - Zoheir Heshmatipour
- Department of Microbiology, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran
| | - Mirsasan Mirpour
- Department of Microbiology, Lahijan Branch, Islamic Azad University, Lahijan, Iran
| | - Saeid Zarrabi
- Department of Chemistry, Lahijan Branch, Islamic Azad University, Lahijan, Iran
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30
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Gamie Z, Karthikappallil D, Gamie E, Stamiris S, Kenanidis E, Tsiridis E. Molecular sequencing technologies in the diagnosis and management of prosthetic joint infections. Expert Rev Mol Diagn 2021; 22:603-624. [PMID: 33641572 DOI: 10.1080/14737159.2021.1894929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Prosthetic joint infections (PJIs) can be challenging to eradicate and have high morbidity and mortality. Current microbiology culture methods can be associated with a high false-negative rate of up to 50%. Early and accurate diagnosis is crucial for effective treatment, and negative results have been linked to a greater rate of reoperation. AREAS COVERED There has been increasing investigation of the use of next-generation sequencing (NGS) technology such as metagenomic shotgun sequencing to help identify causative organisms and decrease the uncertainty around culture-negative infections. The clinical importance of the organisms detected and their management, however, requires further study. The polymerase chain reaction (PCR) has shown promise, but in recent years multiple studies have reported similar or lower sensitivity for bacteria detection in PJIs when compared to traditional culture. Furthermore, issues such as high cost and complexity of sample preparation and data analysis are to be addressed before it can move further toward routine clinical practice. EXPERT OPINION Metagenomic NGS has shown results that inspire cautious optimism - both in culture-positive and culture-negative cases of joint infection. Refinement of technique could revolutionize the way PJIs are diagnosed, managed, and drastically improve outcomes from this currently devastating complication.
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Affiliation(s)
- Zakareya Gamie
- Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK; Genomic Medicine - St George's, University of London, Cranmer Terrace, Tooting, London, SW17 0RE; King's College London, Strand, London
| | - Dileep Karthikappallil
- Department of Trauma and Orthopedics, East Cheshire NHS Trust, Macclesfield District General Hospital, Victoria Road, Macclesfield, Cheshire, SK10 3BL, UK
| | - Emane Gamie
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; MBiol, BSc Biological Sciences, University of Leeds Alumni, UK
| | - Stavros Stamiris
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
| | - Eustathios Kenanidis
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
| | - Eleftherios Tsiridis
- Academic Orthopedic Department, Papageorgiou General Hospital, Thessaloniki, Greece; CORE-Center for Orthopedic Research at CIRI-A.U.Th., Aristotle University Medical School, Thessaloniki, Greece
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Development and evaluation of a nanopore 16S rRNA gene sequencing service for same day targeted treatment of bacterial respiratory infection in the intensive care unit. J Infect 2021; 83:167-174. [PMID: 34146598 DOI: 10.1016/j.jinf.2021.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 01/16/2023]
Abstract
OBJECTIVES Assess the feasibility and impact of nanopore-based 16S rRNA gene sequencing (Np16S) service on antibiotic treatment for acute severe pneumonia on the intensive care unit (ICU). METHODS Speciation and sequencing accuracy of Np16S on isolates with bioinformatics pipeline optimisation, followed by technical evaluation including quality checks and clinical-reporting criteria analysing stored respiratory samples using single-sample flow cells. Pilot service comparing Np16S results with all routine respiratory tests and impact on same-day antimicrobial prescribing. RESULTS Np16S correctly identified 140/167 (84%) isolates after 1h sequencing and passed quality control criteria including reproducibility and limit-of-detection. Sequencing of 108 stored respiratory samples showed concordance with routine culture in 80.5% of cases and established technical and clinical reporting criteria. A 10-week same-day pilot Np16S service analysed 45 samples from 37 patients with suspected community (n=15) or hospital acquired (n=30) pneumonia. Np16S showed concordance compared with all routine culture or molecular tests for 27 (82%) of 33 positive samples. It identified the causative pathogen in 32/33 (97%) samples and contributed to antimicrobial treatment changes for 30 patients (67%). CONCLUSIONS This study demonstrates feasibility of providing a routine same-day nanopore sequencing service that makes a significant contribution to early antibiotic prescribing for bacterial pneumonia in the ICU.
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[Diagnosis of periprosthetic joint infection : Development of an evidence-based algorithm by the work group of implant-associated infection of the AE-(German Society for Arthroplasty)]. DER ORTHOPADE 2021; 50:312-325. [PMID: 32666142 PMCID: PMC7990870 DOI: 10.1007/s00132-020-03940-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hintergrund Die Behandlung periprothetischer Infektionen (PPI) ist eine der größten Herausforderungen im Bereich der Endoprothetik. Der möglichst sichere Ausschluss oder die Bestätigung einer periprothetischen Infektion ist die Voraussetzung für jede Revisionsoperation und kann für den behandelnden Orthopäden und Unfallchirurgen eine große Herausforderung darstellen. Eine sichere evidenzbasierte präoperative Diagnostik ist im Sinne des Patienten notwendig, um einerseits eine periprothetische Infektion zu erkennen sowie die entsprechende chirurgische und antibiotische Therapie zu planen und andererseits unnötige zweizeitige Wechsel zu vermeiden. Ziel der Arbeit Ziel ist es, ein evidenzbasiertes problem- und prioritätenbasiertes Vorgehen zu entwickeln und dies in einem transparenten und standardisierten Algorithmus zusammenzufassen. Methode Durch systematische Literaturrecherche wurden relevante Arbeiten identifiziert und im Rahmen von Expertenrunden bewertet. Nach Extraktion der Daten erfolgte die Berechnung von Sensitivität, Spezifität, positiver und negativer Likelihood-Ratio sowie positiver und negativer prädiktiver Werte. Im Rahmen von 4 Treffen wurden die entsprechenden Studien der Arbeitsgruppe für implantatassoziierte Infektionen präsentiert und analog zu Standard-Delphi-Runden durch die einzelnen Experten bearbeitet und bewertet. Gemäß der Prioritätenliste der Expertenrunde erfolgte die Entwicklung eines zur ISO (International Organization for Standardisation) konformen Algorithmus. Ergebnisse Der entwickelte Algorithmus ist eine Abfolge von evidenzbasierten Prozessen gemäß der verwendeten ISO-Norm. Gemäß der durch die Expertenrunde priorisierten Haupt- und Nebenkriterien erfolgte die Entwicklung logisch strukturiert und problemorientiert. Schlussfolgerung Der Ausschluss einer periprothetischen Infektion ist von enormer Bedeutung vor einer Revisionsoperation und entscheidet in vielen Fällen über den Erfolg und die Invasivität der Operation. Die Diagnose „periprothetische Infektion“ erfordert eine substanzielle Veränderung der therapeutischen Strategie. Der durch die Arbeitsgruppe entwickelte Algorithmus fasst Positionen aus der aktuellen Literatur und spezielle Expertenmeinungen zusammen, dies ermöglicht einen transparenten diagnostischen Ansatz im Sinne einer Standard Operation Procedure.
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Paz Z, Zhu C, Lieber SB, Fowler ML, Shmerling RH. Presentation and Outcomes of Peri-Prosthetic Joint Infection: A Comparison of Culture-Positive and Culture-Negative Disease. Surg Infect (Larchmt) 2021; 22:828-835. [PMID: 33689447 DOI: 10.1089/sur.2020.302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Peri-prosthetic joint infection (PJI) is a debilitating and costly complication of joint replacement. Synovial fluid cultures are negative in up to 25% of PJI cases. The purpose of this study was to compare the clinical characteristics and outcomes of culture negative and culture positive PJI. Patients and Methods: We conducted a retrospective study including all patients aged 18 and older admitted to a single tertiary-care hospital between 1998 and 2015 diagnosed with PJI and treated with antibiotic agents and surgery. Results: One hundred ninety-six patients with PJI were identified; 48 (24.5%) were culture-negative (CN) and 148 (75.5%) were culture-positive (CP). The groups were similar in age and presence of associated comorbidities. Fever was more common among the CP patients (CN, 23.8%; CP, 38.4%; p = 0.03) as was sepsis defined by Sepsis-2 criteria (CN, 12.8%; CP, 28.7%; p = 0.03). Patients who were CP had higher synovial white blood cell (WBC) count (CN, 30,500 per milliliter; CP, 95,400 per milliliter; p < 0.01), a longer length of stay (CN, 3.8%; CP,7.9%; p = 0.02), and fewer alternative diagnoses established within one year (CN, 25.0%; CP, 2.7%; p < 0.01). Our logistic regression models also found that CP patients had an adjusted odds ratio (OR) of 2.59 for rehabilitation placement with 95% confidence interval (CI) of 1.15-5.83 and adjusted OR of 0.04 for an alternative diagnosis within one year with 95% CI, 0.009-0.22 compared with their CN counterparts. Conclusions: This study suggests that patients with CN PJI have less severe disease, better outcomes, and higher rates of alternative diagnoses within one year.
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Affiliation(s)
- Ziv Paz
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Clara Zhu
- Boston University School of Medicine, Boston, Massachusetts, USA
| | - Sarah B Lieber
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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Shibraen MH, Ibrahim OM, Asad RA, Yang S, El-Aassar M. Interpenetration of metal cations into polyelectrolyte-multilayer-films via layer-by-layer assembly: Selective antibacterial functionality of cationic guar gum/ polyacrylic acid- Ag+ nanofilm against resistant E. coli. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2020.125921] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Esteban J, Gómez-Barrena E. An update about molecular biology techniques to detect orthopaedic implant-related infections. EFORT Open Rev 2021; 6:93-100. [PMID: 33828851 PMCID: PMC8022009 DOI: 10.1302/2058-5241.6.200118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Despite different criteria to diagnose a prosthetic joint infection (PJI), aetiological diagnosis of the causing microorganism remains essential to guide treatment.Molecular-biology-based PJI diagnosis is progressing (faster, higher specificity) in different techniques, from the experimental laboratory into clinical use.Multiplex polymerase chain reaction techniques (custom-made or commercial) provide satisfactory results in clinical series of cases, with specificity close to 100% and sensitivity over 70-80%.Next-generation metagenomics may increase sensitivity while maintaining high specificity.Molecular biology techniques may represent, in the next five years, a significant transformation of the currently available microbiological diagnosis in PJI. Cite this article: EFORT Open Rev 2021;6:93-100. DOI: 10.1302/2058-5241.6.200118.
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Affiliation(s)
- Jaime Esteban
- Servicio de Microbiología Clínica, Hospital Universitario Fundación Jiménez Díaz-IIS-Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Enrique Gómez-Barrena
- Servicio de Cirugía Ortopédica y Traumatología, Hospital Universitario La Paz-IdiPaz, Universidad Autónoma de Madrid, Madrid, Spain
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Kildow BJ, Ryan SP, Danilkowicz R, Lazarides AL, Penrose C, Bolognesi MP, Jiranek W, Seyler TM. Next-generation sequencing not superior to culture in periprosthetic joint infection diagnosis. Bone Joint J 2021; 103-B:26-31. [PMID: 33380207 DOI: 10.1302/0301-620x.103b1.bjj-2020-0017.r3] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AIMS Use of molecular sequencing methods in periprosthetic joint infection (PJI) diagnosis and organism identification have gained popularity. Next-generation sequencing (NGS) is a potentially powerful tool that is now commercially available. The purpose of this study was to compare the diagnostic accuracy of NGS, polymerase chain reaction (PCR), conventional culture, the Musculoskeletal Infection Society (MSIS) criteria, and the recently proposed criteria by Parvizi et al in the diagnosis of PJI. METHODS In this retrospective study, aspirates or tissue samples were collected in 30 revision and 86 primary arthroplasties for routine diagnostic investigation for PJI and sent to the laboratory for NGS and PCR. Concordance along with statistical differences between diagnostic studies were calculated. RESULTS Using the MSIS criteria to diagnose PJI as the reference standard, the sensitivity and specificity of NGS were 60.9% and 89.9%, respectively, while culture resulted in sensitivity of 76.9% and specificity of 95.3%. PCR had a low sensitivity of 18.4%. There was no significant difference based on sample collection method (tissue swab or synovial fluid) (p = 0.760). There were 11 samples that were culture-positive and NGS-negative, of which eight met MSIS criteria for diagnosing infection. CONCLUSION In our series, NGS did not provide superior sensitivity or specificity results compared to culture. PCR has little utility as a standalone test for PJI diagnosis with a sensitivity of only 18.4%. Currently, several laboratory tests for PJI diagnosis should be obtained along with the overall clinical picture to help guide decision-making for PJI treatment. Cite this article: Bone Joint J 2021;103-B(1):26-31.
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Affiliation(s)
- Beau J Kildow
- Department of Orthopaedic Surgery, Duke University, Durham, North Carolina, USA
| | - Sean P Ryan
- Department of Orthopaedic Surgery, Duke University, Durham, North Carolina, USA
| | - Richard Danilkowicz
- Department of Orthopaedic Surgery, Duke University, Durham, North Carolina, USA
| | | | - Colin Penrose
- Department of Orthopaedic Surgery, Duke University, Durham, North Carolina, USA
| | - Michael P Bolognesi
- Department of Orthopaedic Surgery, Duke University, Durham, North Carolina, USA
| | - William Jiranek
- Department of Orthopaedic Surgery, Duke University, Durham, North Carolina, USA
| | - Thorsten M Seyler
- Department of Orthopaedic Surgery, Duke University, Durham, North Carolina, USA
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Gholamhosseini A, Sharifiyazdi H, Rakhshaninejad M, Soltanian S, Salighehzadeh R, Kordestani H. A study on the oral and cloacal bacterial flora of Mugger crocodiles ( Crocodylus palustris) in the Negour protected area, Iran. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2021; 12:361-367. [PMID: 34815849 PMCID: PMC8576159 DOI: 10.30466/vrf.2019.108417.2571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/29/2019] [Indexed: 11/23/2022]
Abstract
Mugger crocodile is the only crocodile existing in Iran. The present study was aimed to investigate the bacterial flora in oral and cloacal cavities of wild Mugger crocodiles in Negour protected area, Iran. The isolation and molecular characterization of oral and cloacal bacterial flora were performed in 22 Mugger crocodiles captured in Negour protected area, Iran. Ten bacterial species from all oral samples and six bacterial species from all cloacal samples were recovered. The most commonly isolated bacteria in oral samples were Burkholderia contaminans and Lactococcus garvieae, respectively; whereas, in cloacal samples, it was Lactococcus lactis. It is likely that the isolated bacteria would pose a threat to both crocodiles and humans health. It can threaten crocodiles during stressful conditions; while, humans would be susceptible if they are bitten by crocodiles, consume their meat or spend time near their natural environment. This study provides useful information about bacterial diversity which could help to select the most appropriate anti-bacterial when dealing with infections caused by crocodiles.
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Affiliation(s)
- Amin Gholamhosseini
- Correspondence Amin Gholamhosseini. DVM, PhD, Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran. E-mail: Reza Salighehzadeh. PhD, Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran. E-mail:
| | | | | | | | - Reza Salighehzadeh
- Correspondence Amin Gholamhosseini. DVM, PhD, Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran. E-mail: Reza Salighehzadeh. PhD, Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran. E-mail:
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Sanz-Ruiz P, Matas-Diez JA, Villanueva-Martínez M, Santos-Vaquinha Blanco AD, Vaquero J. Is Dual Antibiotic-Loaded Bone Cement More Effective and Cost-Efficient Than a Single Antibiotic-Loaded Bone Cement to Reduce the Risk of Prosthetic Joint Infection in Aseptic Revision Knee Arthroplasty? J Arthroplasty 2020; 35:3724-3729. [PMID: 32682594 DOI: 10.1016/j.arth.2020.06.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Higher rates of prosthetic joint infections (PJIs) are related to patient risk factors and/or to special surgical procedures such as revision total knee arthroplasty (rTKA). Among the measures discussed to better protect those patients from the higher infection risks use of dual antibiotic-loaded bone cement has emerged as a further prophylactic option. METHODS This retrospective study included 246 patients undergoing strictly aseptic revision knee arthroplasty at our institution in the time period 2015-2018. Based on the type of bone cement used for the cementation of the revision prosthesis, 2 groups were defined. In total, 143 patients received the low-dose single antibiotic-loaded bone cement (SALBC) PALACOS R+G and 103 patients received the high-dose dual antibiotic-loaded bone cement (DALBC) COPAL G+C. The number of PJI cases in each group over a follow-up time of minimum 1 year was compared and the extra costs for the DALBC use calculated against the economic savings per each avoided PJI case on basis of 3 different assumptions (treatment costs and amount of cement use). RESULTS Use of DALBC in aseptic rTKA was associated with a significant reduction in PJI cases (relative risk = 57%, PJI rate in the SALBC group 4.1% vs 0% in the DALBC group, P = 0.035). The calculated total savings per patient was $1367. Depending on the economic assumptions the range of savings was between $1413 (less favorable calculation model) and $3661 (most favorable calculation model). CONCLUSION The use of DALBC in rTKA has been found to be more effective in preventing PJI and proved cost-efficient in all our cost-calculation models.
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Affiliation(s)
- Pablo Sanz-Ruiz
- Department of Traumatology and Orthopaedic Surgery, General University Hospital Gregorio Marañón, Madrid, Spain; Faculty of Medicine, Complutense University of Madrid, Madrid, Spain
| | - José Antonio Matas-Diez
- Department of Traumatology and Orthopaedic Surgery, General University Hospital Gregorio Marañón, Madrid, Spain
| | | | | | - Javier Vaquero
- Department of Traumatology and Orthopaedic Surgery, General University Hospital Gregorio Marañón, Madrid, Spain; Faculty of Medicine, Complutense University of Madrid, Madrid, Spain
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Baldan R, Sendi P. Precision Medicine in the Diagnosis and Management of Orthopedic Biofilm Infections. Front Med (Lausanne) 2020; 7:580671. [PMID: 33240905 PMCID: PMC7683765 DOI: 10.3389/fmed.2020.580671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/22/2020] [Indexed: 01/02/2023] Open
Abstract
Orthopedic biofilm infections are difficult to treat and require a multidisciplinary approach to diagnostics and management. Recent advances in the field include methods to disrupt biofilm, sequencing tools, and antibiotic susceptibility tests for bacteria residing in biofilm. The observation of interclonal differences in biofilm properties of the causative microorganisms, together with considerations of comorbidities and polypharmacy in a growing aging population, calls for a personalized approach to treat these infections. In this article, we highlight aspects of precision medicine that may open new perspectives in the diagnosis and management of orthopedic biofilm infections.
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Affiliation(s)
- Rossella Baldan
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Centre for Musculoskeletal Infections, University Hospital Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, Departments of Medicine and Clinical Research, University Hospital Basel, Basel, Switzerland.,Department of Orthopaedic and Trauma Surgery, University Hospital Basel, Basel, Switzerland
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Kildow BJ, Ryan SP, Danilkowicz R, Lazarides AL, Vovos TJ, Bolognesi MP, Jiranek WA, Seyler TM. Commercially Available Polymerase Chain Reaction Has Minimal Utility in the Diagnosis of Periprosthetic Joint Infection. Orthopedics 2020; 43:333-338. [PMID: 33002175 DOI: 10.3928/01477447-20200923-01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/10/2020] [Indexed: 02/03/2023]
Abstract
The use of genetic sequencing modalities in the diagnosis of periprosthetic joint infection (PJI) and the identification of organisms has gained popularity recently. Polymerase chain reaction (PCR) offers timely results for common organisms. The purpose of this study was to compare the accuracy of broad-range PCR, conventional culture, the Musculoskeletal Infection Society (MSIS) criteria, and the recently proposed criteria by Parvizi et al in the diagnosis of PJI. In this retrospective study, aspirate or tissue samples were collected in 104 revision and 86 primary arthroplasties for routine diagnostic workup for PJI and sent to the laboratory for PCR. Concordance along with statistical differences between diagnostic studies were calculated using chi-square test for categorical data. On comparison with the MSIS criteria, concordance was significantly lower for PCR at 64.7% compared with 86.3% for culture (P<.001). There was no significant difference based on diagnosis of prior infection (P=.706) or sample collection method (tissue swab or synovial fluid) (P=.316). Of the 87 patients who met MSIS criteria, only 20 (23.0%) PCR samples had an organism identified. In this series, PCR had little utility as a stand-alone test for the diagnosis of PJI, with a sensitivity of only 23.0% when using MSIS criteria as the gold standard. Polymerase chain reaction also appears to be significantly less accurate than culture in the diagnosis of PJI. Currently, several laboratory tests used for either criteria for PJI diagnosis should be obtained along with the overall clinical picture to help guide decision-making for PJI treatment. [Orthopedics. 2020;43(6):333-338.].
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First evaluation of the automated-multiplex-PCR Unyvero ITI G2 cartridge for rapid diagnosis of osteo-articular infections. Infect Dis Now 2020; 51:179-186. [PMID: 33010353 DOI: 10.1016/j.medmal.2020.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/28/2020] [Accepted: 09/24/2020] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Conventional microbiological methods (CMM), including long-term culture, for the diagnosis of osteo-articular infections (OAI) fail in at least 5% of all cases. Only one IOA dedicated molecular method has been commercialized, and only the first version of this kit has been studied. The aim of this work was to evaluate the concordance between test results obtained with the second version of the Unyvero ITI G2 cartridge (Curetis) and CMM. The cartridge, combining one-step automated lysis/DNA extraction with multiplex PCR and amplicon detection by array hybridization, allows for the detection of 102 prevalent pathogens and their antibiotic resistance markers directly in clinical specimens (liquid [n=8] or solid [n=32]). MATERIAL AND METHODS Frozen samples from 40 patients who underwent orthopedic surgery at Pitié-Salpêtrière hospital were tested retrospectively with the cartridge: 5 were culture-negative, 25 revealed monomicrobial and 10 polymicrobial OAI. The 2 main surgical sites were hip (22.5%) and knee (17.5%). RESULTS Extraction, amplification and hybridization reactions were completed in 28 of the 40 cases, failed in all cartridge chambers in 6 cases, and in 1 or 2 chambers in an additional 6 cases. Overall sensitivity and specificity for microorganism identification were estimated at 67.6% and 98.2%, when complete and partial failures were excluded. CONCLUSIONS These results show that the performances of the second version of the Unyvero ITI G2 cartridge should be further enhanced before considering avoiding conventional microbiological methods.
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He R, Wang Q, Zhang F, Tang J, Shen H, Zhang X. Metagenomic sequencing in the management of fungal periprosthetic joint infection. J Infect 2020; 81:816-846. [PMID: 32956727 DOI: 10.1016/j.jinf.2020.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Renke He
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's, Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China
| | - Qiaojie Wang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's, Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China
| | - Feiyang Zhang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's, Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China
| | - Jin Tang
- Department of Clinical Laboratory, Shanghai Jiao Tong University Affiliated Sixth, People's Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China
| | - Hao Shen
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's, Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China.
| | - Xianlong Zhang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's, Hospital, Shanghai Jiao Tong University, Shanghai 200233, PR China.
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Zhang Y, Feng S, Chen W, Zhang QC, Shi SF, Chen XY. Advantages of 16S rRNA PCR for the diagnosis of prosthetic joint infection. Exp Ther Med 2020; 20:3104-3113. [PMID: 32855678 PMCID: PMC7444347 DOI: 10.3892/etm.2020.9082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/24/2020] [Indexed: 11/06/2022] Open
Abstract
16S ribosomal RNA (rRNA) PCR has been reported to be an effective diagnostic means in patients with prosthetic joint infection (PJI). The aim of the present meta-analysis is to establish the overall diagnostic accuracy of the measurement of 16S rRNA PCR for diagnosing PJI. PubMed, Web of Science, Cochrane Library, EMBASE and Wiley Online Library were searched for studies on 16S rRNA PCR in the diagnosis of PJI. The search incorporated all literature published up until December 2018 and the QUADAS-2 checklist were used for quality assessment. The sensitivity, specificity and other measures of accuracy of 16S rRNA PCR in the diagnosis of PJI were pooled. Statistical analysis was performed by employing Meta-Disc 1.4 and Stata 12.0 software. A total of 15 studies met the inclusion criteria. The summary estimates for 16S rRNA PCR in the diagnosis of PJI in these studies were pooled: Sensitivity, 0.70 (95% CI, 0.67-0.73); specificity, 0.93 (95% CI, 0.91-0.94); positive likelihood ratio, 10.93 (95% CI, 5.55-21.51); negative likelihood ratio, 0.33 (95% CI, 0.28-0.40); diagnostic odds ratio, 41.77 (95% CI, 19.90-87.68); and the area under the curve, 0.89. Subgroup analysis showed that the use of sonicate fluid and periprosthetic tissue has higher sensitivity (0.76; 95% CI, 0.69-0.82; and 0.73; 95% CI, 0.68-0.78, respectively), specificity (0.93, 95% CI, 0.90-0.96; and 0.95; 95% CI, 0.90-0.98, respectively) and area under the curve (0.93 and 0.98, respectively). 16S rRNA PCR assay plays an important role in the diagnosis of PJI. The results of 16S rRNA PCR assays should be interpreted in parallel with clinical findings, the results of microbiological, and other laboratory tests.
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Affiliation(s)
- Ye Zhang
- Department of Orthopedic Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Shuo Feng
- Department of Orthopedic Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Wang Chen
- Department of Orthopedic Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Qing-Chen Zhang
- Department of Orthopedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Si-Feng Shi
- Department of Orthopedic Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Xiang-Yang Chen
- Department of Orthopedic Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
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Rockov ZA, Clarke HD, Grys TE, Chang YHH, Schwartz AJ. Is There an Optimal Cutoff for Aspiration Fluid Volume in the Diagnosis of Periprosthetic Joint Infection? J Arthroplasty 2020; 35:2217-2222. [PMID: 32269007 DOI: 10.1016/j.arth.2020.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/11/2020] [Accepted: 03/05/2020] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The diagnosis of periprosthetic joint infection is often challenging in the setting of low aspiration volumes, or in the presence of infection with a slow-growing organism. We sought to determine if an optimal threshold of aspiration fluid volume exists when cultures from the preoperative aspiration are compared to intraoperative cultures. METHODS All revision total hip and knee arthroplasty procedures over 5 years at our institution were reviewed. Cases were excluded if they underwent joint lavage during aspiration, had an antibiotic spacer in place, were suspected of adverse local tissue reaction to metal debris, did not have an accurate aspiration volume recorded, or if there were no aspiration or operative cultures available. Receiver operating characteristic curves were used to evaluate aspiration volume for identifying cases with identical aspiration and culture results. RESULTS A total of 857 revision cases were reviewed, among which 294 met inclusion criteria. There were 45 cases (15.3%) with discordant aspiration and operative cultures. The mean aspiration volume for identical cases was significantly higher than for discordant cases (19.1 vs 10.2 mL, P = .02). The proportion of slow-growing organisms was significantly greater among discordant compared to identical operative cultures (52.4% for discordant cases vs 8.2% for identical cases, P < .001). The optimal cutoff value for predicting identical cultures was 3.5 mL for typical organisms and 12.5 mL for slow-growing organisms. CONCLUSION Aspiration cultures are more likely to correlate with intraoperative cultures with higher aspiration volumes, and the optimal aspiration volume is higher for slow-growing organisms.
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Affiliation(s)
- Zachary A Rockov
- Department of Orthopaedic Surgery, Mayo Clinic Arizona, Phoenix, AZ
| | - Henry D Clarke
- Department of Orthopaedic Surgery, Mayo Clinic Arizona, Phoenix, AZ
| | - Thomas E Grys
- Department of Microbiology, Mayo Clinic Arizona, Phoenix, AZ
| | - Yu-Hui H Chang
- Department of Biostatistics, Mayo Clinic Arizona, Phoenix, AZ
| | - Adam J Schwartz
- Department of Orthopaedic Surgery, Mayo Clinic Arizona, Phoenix, AZ
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Draft Genome Sequence of a Lactobacillus fermentum Strain Isolated from Domestic Sewage in Kerala, India. Microbiol Resour Announc 2020; 9:9/29/e00713-20. [PMID: 32675192 PMCID: PMC7365803 DOI: 10.1128/mra.00713-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the draft genome sequence of a putative probiotic strain, Lactobacillus fermentum ASBT-2, isolated from domestic sewage in Kerala, India. The strain showed probiotic properties (tolerance to low pH and bile salts, binding to host matrix) and reduced the coliform count by 90% in a biofilter used to treat wastewater. We report the draft genome sequence of a putative probiotic strain, Lactobacillus fermentum ASBT-2, isolated from domestic sewage in Kerala, India. The strain showed probiotic properties (tolerance to low pH and bile salts, binding to host matrix) and reduced the coliform count by 90% in a biofilter used to treat wastewater.
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Peel TN, de Steiger R. How to manage treatment failure in prosthetic joint infection. Clin Microbiol Infect 2020; 26:1473-1480. [PMID: 32619734 DOI: 10.1016/j.cmi.2020.06.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/16/2020] [Accepted: 06/20/2020] [Indexed: 02/01/2023]
Abstract
BACKGROUND Management for prosthetic joint infections remains a challenging area for both infectious diseases and orthopaedic surgery, particularly in the setting of treatment failure. This is compounded by a lack of level 1 evidence to guide approaches. The optimal management of prosthetic joint infections requires a multi-disciplinary approach combined with shared decision making with the patient. AIMS This article describes the approach to prosthetic joint infections in the setting of treatment failure. SOURCES Narrative review based on literature review from PubMed. There was no time limit on the studies included. In addition, the reference list for included studies were reviewed for literature saturation with manual searching of clinical guidelines. Management approaches described incorporate evidence- and eminence-based recommendations from expert guidelines and clinical studies, where applicable. CONTENT The surgical and antimicrobial approaches for prosthetic joint infections are described for first-line treatment of prosthetic joint infections and approaches in the event of treatment failure. Management approaches are based on an understanding of the role the biofilm plays in the pathogenesis of prosthetic joint infections. The management of these infections aims to fulfil two key goals: to eradicate the biofilm-associated microorganisms and, to maintain a functional joint and quality of life. In treatment failure, these goals are not always feasible, and the role of the multi-disciplinary team and shared-decision making are prominent. IMPLICATIONS Prosthetic joint surgery is a high-volume surgery, and the demand for this surgery is continually increasing. With this, the number of infections requiring expert care will also increase. Eminence-based management approaches have been established to guide treatment failure until knowledge gaps in optimal management are addressed by well-designed, clinical trials.
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Affiliation(s)
- T N Peel
- Department of Infectious Diseases, Monash University and Alfred Health, Melbourne, Victoria, Australia.
| | - R de Steiger
- Department of Surgery, Epworth Healthcare, The University of Melbourne, Victoria, Australia
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Comprehensive depiction of novel heavy metal tolerant and EPS producing bioluminescent Vibrio alginolyticus PBR1 and V. rotiferianus PBL1 confined from marine organisms. Microbiol Res 2020; 238:126526. [PMID: 32603934 DOI: 10.1016/j.micres.2020.126526] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/27/2020] [Accepted: 06/09/2020] [Indexed: 01/09/2023]
Abstract
The current study depicts the isolation of luminescent bacteria from fish and squid samples that were collected from Veraval fish harbour. From Indian mackerel, total 14 and from squid, total 23 bioluminescent bacteria were isolated using luminescence agar medium. Two bioluminescent bacteria with highest relative luminescence intensity PBR1 and PBL1 were selected. These two isolates were subjected to detailed biochemical characterization and were tested positive for 5 out of 13 biochemical tests. Furthermore, both PBR1 and PBL1 were able to ferment cellobiose, dextrose, fructose, galactose, maltose, mannose, sucrose and trehalose with acid production. Based on 16S rRNA partial gene sequence analysis, PBR1 was identified as Vibrio alginolyticus and PBL1 as V. rotiferianus. Antibiotic susceptibility test using paper-disc method showed that PBR1 and PBL1 were sensitive to chloramphenicol, ciprofloxacin, co-trimoxazole, gatifloxacin, levofloxacin, linezolid ad roxithromycin out of 18 antibiotics tested. Moreover, both strains were evaluated for their exopolysachharide (EPS) producing ability where PBR1 and PBL1 were able to yield 1.34 g% (w/v) and 2.45 g% (w/v) EPS respectively from 5 g% (v/v) sucrose concentration. Heavy metal toxicity assessment was carried out using agar well diffusion method with eight heavy metals and both the strains were sensitive to As(III), Cd(II), Ce(II), Cr(III), Cu(II), Hg(II) and while they showed resistance to Pb(II) and Sr(II). Based on these results, a study was conducted to demonstrate bio-removal of Pb and Sr by EPS of PBR1 and PBL1. Fourier transform infrared (FTIR) spectra revealed the functional groups of EPS involved in interaction with the heavy metals. Owing to the sensitivity for the remaining heavy metals, these bioluminescent bacteria can be used further for the development of luminescence-based biosensor.
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Chan WS, Chan TL, Au CH, Leung CP, To MY, Ng MK, Leung SM, Chan MKM, Ma ESK, Tang BSF. An economical Nanopore sequencing assay for human papillomavirus (HPV) genotyping. Diagn Pathol 2020; 15:45. [PMID: 32375813 PMCID: PMC7203875 DOI: 10.1186/s13000-020-00964-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/28/2020] [Indexed: 12/28/2022] Open
Abstract
Background Human papillomavirus (HPV) testing has been employed by several European countries to augment cytology-based cervical screening programs. A number of research groups have demonstrated potential utility of next-generation sequencing (NGS) for HPV genotyping, with comparable performance and broader detection spectrum than current gold standards. Nevertheless, most of these NGS platforms may not be the best choice for medium sample throughput and laboratories with less resources and space. In light of this, we developed a Nanopore sequencing assay for HPV genotyping and compared its performance with cobas HPV Test and Roche Linear Array HPV Genotyping Test (LA). Methods Two hundred and one cervicovaginal swabs were routinely tested for Papanicolaou smear, cobas HPV Test and LA. Residual DNA was used for Nanopore protocol after routine testing. Briefly, HPV L1 region was amplified using PGMY and MGP primers, and PCR-positive specimens were sequenced on MinION flow cells (R9.4.1). Data generated in first 2 h were aligned with reference sequences from Papillomavirus Episteme database for genotyping. Results Nanopore detected 96 HPV-positive (47.76%) and 95 HPV-negative (47.26%) specimens, with 10 lacking β-globin band and not further analyzed (4.98%). Substantial agreement was achieved with cobas HPV Test and LA (κ: 0.83–0.93). In particular, Nanopore appeared to be more sensitive than cobas HPV Test for HPV 52 (n = 7). For LA, Nanopore revealed higher concordance for high-risk (κ: 0.93) than non-high risk types (κ: 0.83), and with similar high-risk positivity in each cytology grading. Nanopore also provided better resolution for HPV 52 in 3 specimens co-infected with HPV 33 or 58, and for HPV 87 which was identified as HPV 84 by LA. Interestingly, Nanopore identified 5 additional HPV types, with an unexpected high incidence of HPV 90 (n = 12) which was reported in North America and Belgium but not in Hong Kong. Conclusions We developed a Nanopore workflow for HPV genotyping which was economical (about USD 50.77 per patient specimen for 24-plex runs), and with comparable or better performance than 2 reference methods in the market. Future prospective study with larger sample size is warranted to further evaluate test performance and streamline the protocol.
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Affiliation(s)
- Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Chun Hang Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Chin Pang Leung
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Man Yan To
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Man Kin Ng
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Sau Man Leung
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - May Kwok Mei Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China.
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Chan WS, Au CH, Leung SM, Ho DN, Wong EYL, To MY, Ng MK, Chan TL, Ma ESK, Tang BSF. Potential utility of targeted Nanopore sequencing for improving etiologic diagnosis of bacterial and fungal respiratory infection. Diagn Pathol 2020; 15:41. [PMID: 32340617 PMCID: PMC7184685 DOI: 10.1186/s13000-020-00960-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
Background Diversified etiology of lower respiratory tract infection renders diagnosis challenging. The mainstay microbial culture is time-consuming and constrained by variable growth requirements. In this study, we explored the use of Nanopore sequencing as a supplementary tool to alleviate this diagnostic bottleneck. Methods We developed a targeted Nanopore method based on amplification of bacterial 16S rRNA gene and fungal internal transcribed spacer region. The performance was compared with routine infectious disease workups on 43 respiratory specimens. Results Nanopore successfully identified majority of microbes (47/54, 87.04%) and 7 possible pathogens not detected by routine workups, which were attributable to the content of microbiological investigations (n = 5) and negative culture (n = 2). The average sequencing time for first target reads was 7 min (1–43 min) plus 5 h of pre-sequencing preparation. Conclusions The Nanopore method described here was rapid, economical and hypothesis-free, which might provide valuable hints to further microbiological follow-up for opportunistic pathogens missed or not detectable by conventional tests.
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Affiliation(s)
- Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Chun Hang Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Sau Man Leung
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Dona N Ho
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | | | - Man Kin Ng
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China.
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Gan C, Hu J, Cao Q, Zhao R, Li Y, Wang Z, Tao Y, Mo X. Rapid identification of pathogens involved in pediatric osteoarticular infections by multiplex PCR. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:203. [PMID: 32309350 PMCID: PMC7154398 DOI: 10.21037/atm.2020.01.34] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Background Delays in the diagnosis of pediatric osteoarticular infections (OAIs) can cause associated acute complications or long-term morbidity. This study attempts to develop a multiplex PCR-based assay that can rapidly and accurately detect the main pathogens involved in pediatric OAIs, namely, methicillin-sensitive or methicillin-resistant Staphylococcus aureus, Streptococcus pyogenes and Pseudomonas aeruginosa. Methods A set of four gene-specific primers suitable for use in a one-tube PCR assay was designed to detect four common pathogens involved in pediatric OAIs, namely, nuc for methicillin-sensitive Staphylococcus aureus, nuc and mecA for methicillin-resistant Staphylococcus aureus, spyM for Streptococcus pyogenes and orpI for Pseudomonas aeruginosa. The multiplex PCR was first evaluated with 39 isolated clinical strains and further with 41 specimens collected from patients suspected of having OAIs. Results Specific primer pairs were successfully designed, and the targeted genes were simultaneously amplified. The product sizes in the assay for nuc, mecA, spyM and oprI were 233, 158, 336 and 109 bp, respectively. Evaluation of the multiplex PCR with 39 isolated clinical strains and 41 specimens revealed 100% sensitivity and 100% specificity. The limit of detection of the multiplex PCR assay was approximately 1×103 CFU at the bacterial cell level. Conclusions This newly developed multiplex PCR assay, without sequencing, enables a rapid and accurate diagnosis of the major bacterial species in children with OAIs and might serve as an additional diagnostic approach for urgent pathogen determination.
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Affiliation(s)
- Chi Gan
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Jinfeng Hu
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Qing Cao
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Ruike Zhao
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yuchan Li
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Zhigang Wang
- Department of Pediatric Orthopedics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Yue Tao
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xi Mo
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
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