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Moran A, Arellano J, Bregman K, McElvania E. Evaluation of a BioFire multiplex PCR panel for detection of joint infections using retrospective and prospectively collected specimens. J Clin Microbiol 2024:e0018224. [PMID: 39016560 DOI: 10.1128/jcm.00182-24] [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: 02/03/2024] [Accepted: 06/25/2024] [Indexed: 07/18/2024] Open
Abstract
The BioFire Joint Infection Panel (JI panel) is a newly FDA-approved multiplex PCR assay for detection of common bone and joint pathogens with 39 targets which include select Gram-positive and Gram-negative bacteria, yeast, and antimicrobial resistance genes. We evaluated the performance of the JI panel in detecting joint infections in our patient population. Sixty-three frozen, residual joint fluid specimens were retrospectively tested using the JI panel. An additional 104 residual joint fluid specimens were de-identified and prospectively tested within 1 week of collection. Results from routine bacterial cultures were used as the reference standard, which included inoculation to agar plates and blood culture bottles. For the frozen specimens, the JI panel showed a positive percent agreement (PPA) of 92.8% and a negative percent agreement (NPA) of 97.1%. PPA was 71.4% and NPA was 94.8% for fresh specimens. A total of 12 discrepancies were observed among the 167 specimens tested. The JI panel demonstrated good overall agreement with routine culture for the detection of joint infections and may improve timely diagnosis when used in conjunction with bacterial culture. However, potential false-positive and false-negative results were observed in both retrospective and prospective testing of specimens.IMPORTANCEThe BioFire JI panel is a new commercially available multiplex PCR assay for detecting common pathogens causing bone and joint infections. The test is performed directly on joint fluids with a fast turnaround time of 1 hour. Our study shows that while the JI panel overall shows good agreement with routine culture, discrepancies were observed in 7% of cases and results should be interpreted with appropriate clinical context.
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Affiliation(s)
- Angelica Moran
- Department of Pathology and Laboratory Medicine, Endeavor Health, Evanston, Illinois, USA
- Department of Pathology, University of Chicago, Pritzker School of Medicine, Chicago, Illinois, USA
| | - Jekzaly Arellano
- Department of Pathology and Laboratory Medicine, Endeavor Health, Evanston, Illinois, USA
| | - Karen Bregman
- Department of Pathology and Laboratory Medicine, Endeavor Health, Evanston, Illinois, USA
| | - Erin McElvania
- Department of Pathology and Laboratory Medicine, Endeavor Health, Evanston, Illinois, USA
- Department of Pathology, University of Chicago, Pritzker School of Medicine, Chicago, Illinois, USA
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Gardete-Hartmann S, Mitterer JA, Sebastian S, Frank BJH, Simon S, Huber S, Löw M, Sommer I, Prinz M, Halabi M, Hofstaetter JG. The role of BioFire Joint Infection Panel in diagnosing periprosthetic hip and knee joint infections in patients with unclear conventional microbiological results. Bone Joint Res 2024; 13:353-361. [PMID: 38981611 PMCID: PMC11233181 DOI: 10.1302/2046-3758.137.bjr-2023-0321.r2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/11/2024] Open
Abstract
Aims This study aimed to evaluate the BioFire Joint Infection (JI) Panel in cases of hip and knee periprosthetic joint infection (PJI) where conventional microbiology is unclear, and to assess its role as a complementary intraoperative diagnostic tool. Methods Five groups representing common microbiological scenarios in hip and knee revision arthroplasty were selected from our arthroplasty registry, prospectively maintained PJI databases, and biobank: 1) unexpected-negative cultures (UNCs), 2) unexpected-positive cultures (UPCs), 3) single-positive intraoperative cultures (SPCs), and 4) clearly septic and 5) aseptic cases. In total, 268 archived synovial fluid samples from 195 patients who underwent acute/chronic revision total hip or knee arthroplasty were included. Cases were classified according to the International Consensus Meeting 2018 criteria. JI panel evaluation of synovial fluid was performed, and the results were compared with cultures. Results The JI panel detected microorganisms in 7/48 (14.5%) and 15/67 (22.4%) cases related to UNCs and SPCs, respectively, but not in cases of UPCs. The correlation between JI panel detection and infection classification criteria for early/late acute and chronic PJI was 46.6%, 73%, and 40%, respectively. Overall, the JI panel identified 12.6% additional microorganisms and three new species. The JI panel pathogen identification showed a sensitivity and specificity of 41.4% (95% confidence interval (CI) 33.7 to 49.5) and 91.1% (95% CI 84.7 to 94.9), respectively. In total, 19/195 (9.7%) could have been managed differently and more accurately upon JI panel evaluation. Conclusion Despite its microbial limitation, JI panel demonstrated clinical usefulness by complementing the traditional methods based on multiple cultures, particularly in PJI with unclear microbiological results.
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Affiliation(s)
- Susana Gardete-Hartmann
- Michael Ogon Laboratory for Orthopaedic Research Orthopaedic Hospital Vienna-Speising, Vienna, Austria
| | - Jennyfer A Mitterer
- Michael Ogon Laboratory for Orthopaedic Research Orthopaedic Hospital Vienna-Speising, Vienna, Austria
| | - Sujeesh Sebastian
- Michael Ogon Laboratory for Orthopaedic Research Orthopaedic Hospital Vienna-Speising, Vienna, Austria
| | - Bernhard J H Frank
- Michael Ogon Laboratory for Orthopaedic Research Orthopaedic Hospital Vienna-Speising, Vienna, Austria
| | - Sebastian Simon
- Michael Ogon Laboratory for Orthopaedic Research Orthopaedic Hospital Vienna-Speising, Vienna, Austria
| | - Stephanie Huber
- Michael Ogon Laboratory for Orthopaedic Research Orthopaedic Hospital Vienna-Speising, Vienna, Austria
| | - Marcellino Löw
- Michael Ogon Laboratory for Orthopaedic Research Orthopaedic Hospital Vienna-Speising, Vienna, Austria
| | - Ian Sommer
- Michael Ogon Laboratory for Orthopaedic Research Orthopaedic Hospital Vienna-Speising, Vienna, Austria
| | | | - Milo Halabi
- Institute for Pathology, Microbiology and Molecular Diagnostic, Hospital of the Sisters of Charity, Ried, Austria
| | - Jochen G Hofstaetter
- Michael Ogon Laboratory for Orthopaedic Research Orthopaedic Hospital Vienna-Speising, Vienna, Austria
- 2nd Department, Orthopaedic Hospital Speising, Vienna, Austria
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Subedi S, Isler B, Ezure Y, Furuya-Kanamori L, Eriksson L, Paterson DL, Harris PN. Performance characteristics of genus or species-specific Polymerase Chain Reaction (PCR) for the microbial diagnosis of joint infections: A systematic review and meta-analysis. Diagn Microbiol Infect Dis 2024; 110:116422. [PMID: 38981176 DOI: 10.1016/j.diagmicrobio.2024.116422] [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: 02/01/2024] [Revised: 05/20/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024]
Abstract
Joint infections cause significant morbidity and mortality. Rapid diagnosis enables prompt initiation of appropriate antimicrobial therapy and surgical treatment. We conducted a systematic review and meta-analysis to evaluate the accuracy of genus- or species-specific polymerase chain reaction (PCR) in diagnosing joint infections. The literature databases were searched for articles from January 2010 to December 2022. The meta-analysis using the split component synthesis (SCS) method, included 20 studies with 2,457 adult participants. The pooled sensitivity, specificity, diagnostic odds ratio, and AUC of PCR were 49 % (95 % CI [37.9-60.2]), 95.7 % (95 % CI [91.6-97.8]), 21.32, and 0.82 respectively. Sensitivity was highest for sonicate fluid and lowest for periprosthetic tissue. The mean turnaround time to results was 4.7 hours (SD 1.1). PCR is a favourable option for diagnosing joint infections due to its rapid results, but it has low sensitivity. To enhance diagnostic yield, the test should be used in conjunction with other methods.
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Affiliation(s)
- Shradha Subedi
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane, Australia; Sunshine Coast Hospital and Health Service, Queensland, Australia; Microbiology Laboratory, Pathology Queensland, Queensland, Australia.
| | - Burcu Isler
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane, Australia; Infection Management Service, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Yukiko Ezure
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane, Australia; The School of Public Health, The University of Queensland, Brisbane, Australia
| | - Luis Furuya-Kanamori
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane, Australia
| | - Lars Eriksson
- Herston Health Sciences Library, The University of Queensland, Brisbane, Australia
| | - David L Paterson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane, Australia; ADVANCE-ID, Singapore
| | - Patrick Na Harris
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane, Australia; Microbiology Laboratory, Pathology Queensland, Queensland, Australia
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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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Azad MA, Patel R. Practical Guidance for Clinical Microbiology Laboratories: Microbiologic diagnosis of implant-associated infections. Clin Microbiol Rev 2024; 37:e0010423. [PMID: 38506553 PMCID: PMC11237642 DOI: 10.1128/cmr.00104-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
SUMMARYImplant-associated infections (IAIs) pose serious threats to patients and can be associated with significant morbidity and mortality. These infections may be difficult to diagnose due, in part, to biofilm formation on device surfaces, and because even when microbes are found, their clinical significance may be unclear. Despite recent advances in laboratory testing, IAIs remain a diagnostic challenge. From a therapeutic standpoint, many IAIs currently require device removal and prolonged courses of antimicrobial therapy to effect a cure. Therefore, making an accurate diagnosis, defining both the presence of infection and the involved microorganisms, is paramount. The sensitivity of standard microbial culture for IAI diagnosis varies depending on the type of IAI, the specimen analyzed, and the culture technique(s) used. Although IAI-specific culture-based diagnostics have been described, the challenge of culture-negative IAIs remains. Given this, molecular assays, including both nucleic acid amplification tests and next-generation sequencing-based assays, have been used. In this review, an overview of these challenging infections is presented, as well as an approach to their diagnosis from a microbiologic perspective.
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Affiliation(s)
- Marisa Ann Azad
- Division of Infectious Diseases, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canada
| | - Robin Patel
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Kommedal Ø, Eagan TM, Fløtten Ø, Leegaard TM, Siljan W, Fardal H, Bø B, Grøvan F, Larssen KW, Kildahl-Andersen A, Hjetland R, Tilseth R, Hareide SKØ, Tellevik M, Dyrhovden R. Microbiological diagnosis of pleural infections: a comparative evaluation of a novel syndromic real-time PCR panel. Microbiol Spectr 2024; 12:e0351023. [PMID: 38656204 DOI: 10.1128/spectrum.03510-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/19/2024] [Indexed: 04/26/2024] Open
Abstract
Current microbial diagnostics for pleural infections are insufficient. Studies using 16S targeted next-generation sequencing report that only 10%-16% of bacteria present are cultured and that 50%-78% of pleural fluids containing relevant microbial DNA remain culture negative. As a rapid diagnostic alternative suitable for clinical laboratories, we wanted to explore a PCR-based approach. Based on the identification of key pathogens, we developed a syndromic PCR panel for community-acquired pleural infections (CAPIs). This was a pragmatic PCR panel, meaning that it was not designed for detecting all possibly involved bacterial species but for confirming the diagnosis of CAPI, and for detecting bacteria that might influence choice of antimicrobial treatment. We evaluated the PCR panel on 109 confirmed CAPIs previously characterized using culture and 16S targeted next-generation sequencing. The PCR secured the diagnosis of CAPI in 107/109 (98.2%) and detected all present pathogens in 69/109 (63.3%). Culture secured the diagnosis in 54/109 (49.5%) and detected all pathogens in 31/109 (28.4%). Corresponding results for 16S targeted next-generation sequencing were 109/109 (100%) and 98/109 (89.9%). For bacterial species included in the PCR panel, PCR had a sensitivity of 99.5% (184/185), culture of 21.6% (40/185), and 16S targeted next-generation sequencing of 92.4% (171/185). None of the bacterial species present not covered by the PCR panel were judged to impact antimicrobial therapy. A syndromic PCR panel represents a rapid and sensitive alternative to current diagnostic approaches for the microbiological diagnosis of CAPI.IMPORTANCEPleural empyema is a severe infection with high mortality and increasing incidence. Long hospital admissions and long courses of antimicrobial treatment drive healthcare and ecological costs. Current methods for microbiological diagnostics of pleural infections are inadequate. Recent studies using 16S targeted next-generation sequencing as a reference standard find culture to recover only 10%-16% of bacteria present and that 50%-78% of samples containing relevant bacterial DNA remain culture negative. To confirm the diagnosis of pleural infection and define optimal antimicrobial therapy while limiting unnecessary use of broad-spectrum antibiotics, there is a need for rapid and sensitive diagnostic approaches. PCR is a rapid method well suited for clinical laboratories. In this paper we show that a novel syndromic PCR panel can secure the diagnosis of pleural infection and detect all bacteria relevant for choice of antimicrobial treatment with a high sensitivity.
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Affiliation(s)
- Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Tomas Mikal Eagan
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Øystein Fløtten
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Truls Michael Leegaard
- Division of Medicine and Laboratory Sciences, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Akershus, Norway
| | - William Siljan
- Department of Pulmonary Medicine, Akershus University Hospital, Lorenskog, Akershus, Norway
| | - Hilde Fardal
- Department of Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Bjørnar Bø
- Department of Pulmonary Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Fredrik Grøvan
- Department of Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Kjersti Wik Larssen
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Arne Kildahl-Andersen
- Department of Thoracic Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Reidar Hjetland
- Department of Microbiology, Førde Central Hospital, Førde, Norway
| | - Rune Tilseth
- Department of Medicine, Førde Central Hospital, Førde, Norway
| | | | - Marit Tellevik
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Ruben Dyrhovden
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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Su S, Wang R, Zhou R, Bai J, Chen Z, Zhou F. Higher diagnostic value of next-generation sequencing versus culture in periprosthetic joint infection: A systematic review and meta-analysis. Knee Surg Sports Traumatol Arthrosc 2024. [PMID: 38713871 DOI: 10.1002/ksa.12227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND The next-generation sequencing (NGS) has developed rapidly in the past decade and is becoming a promising diagnostic tool for periprosthetic infection (PJI). However, its diagnostic value for PJI is still uncertain. The purpose of this systematic review and meta-analysis was to evaluate the diagnostic value of NGS compared to culture. METHODS In this systematic review and meta-analysis, electronic databases including PubMed, Embase, Cochrane Central Register of Controlled Trials, Web of Science and clinicaltrials.gov were searched for studies from inception to 12 November 2023. Diagnostic parameters, such as sensitivity, specificity, diagnostic odds ratio and area under the summary receiver-operating characteristic (SROC) curve (AUC), were calculated for the included studies. A systematic review and meta-analysis was performed. RESULTS A total of 22 studies with 2461 patients were included in our study. The pooled sensitivity, specificity and diagnostic odds ratio of NGS were 87% (95% confidence interval [CI]: 83-90), 94% (95% CI: 91-96) and 111 (95% CI: 70-177), respectively. On the other hand, the pooled sensitivity, specificity and diagnostic odds ratio of culture were 63% (95% CI: 58-67), 98% (95% CI: 96-99) and 93 (95% CI: 40-212), respectively. The SROC curve for NGS and culture showed that the AUCs are 0.96 (95% CI: 0.94-0.98) and 0.82 (95% CI: 0.79-0.86), respectively. CONCLUSION This systematic review and meta-analysis found NGS had higher sensitivity and diagnostic accuracy but slightly lower specificity than culture. Based on the pooled results, we suggested NGS may have the potential to be a new tool for the diagnosis of PJI. LEVEL OF EVIDENCE Level IV.
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Affiliation(s)
- Shilong Su
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Ruideng Wang
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Rubing Zhou
- Department of Orthopedics, Beijing friendship hospital, Capital Medical University, Xicheng, Beijing, China
| | - Jinwu Bai
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Zhengyang Chen
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
| | - Fang Zhou
- Department of Orthopedics, Peking University Third Hospital, Haidian, Beijing, China
- Engineering Research Center of Bone and Joint Precision Medicine, Peking University Third Hospital, Haidian, Beijing, China
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Mazzella FM, Zhang Y, Bauer TW. Update on the role of pathology and laboratory medicine in diagnosing periprosthetic infection. Hum Pathol 2024; 147:5-14. [PMID: 38280657 DOI: 10.1016/j.humpath.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/22/2024] [Indexed: 01/29/2024]
Abstract
Technological and implant design advances have helped reduce the frequency of aseptic total joint arthroplasty failure, but periprosthetic joint infections (PJI) remain a clinical important problem with high patient morbidity. Misinterpreting PJI as aseptic mechanical loosening commonly leads to unsatisfactory revision arthroplasty, persistent infection, and poor long-term results. While there is no single "gold standard" diagnostic test for PJI, recent collaborative efforts by Orthopaedic and Infectious Disease Societies have developed algorithms for diagnosing PJI. However, the efficacy of individual tests as well as diagnostic thresholds are controversial. We review the recommended thresholds for commonly used screening tests as well as tissue histopathology and confirmatory tests to diagnose periprosthetic infection. We also update lesser-known laboratory tests, and we briefly summarize rapidly evolving molecular tests to diagnose periprosthetic infection. Pathologists hold a critical role in assisting with PJI diagnosis, maintaining laboratory test quality and interpreting test results. Collaboration between clinicians and pathologists is essential to provide optimal patient care and reduce the burden of PJI.
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Affiliation(s)
- Fermina M Mazzella
- Department of Pathology and Laboratory Medicine, Hospital for Special Surgery, USA
| | - Yaxia Zhang
- Department of Pathology and Laboratory Medicine, Hospital for Sprecial Surgery, Weill Cornell College of Medicine, USA
| | - Thomas W Bauer
- Department of Pathology and Laboratory Medicine, Hospital for Special Surgery, Weill Cornell Medical College, 535 East 70th St, New York, NY, 10021, USA.
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9
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Pascual S, Noble B, Ahmad-Saeed N, Aldridge C, Ambretti S, Amit S, Annett R, O'Shea S, Barbui A, Barlow G, Barrett L, Berth M, Bondi A, Boran N, Boyd S, Chaves C, Clauss M, Davies P, Dianzo-Delgado I, Esteban J, Fuchs S, Friis-Hansen L, Goldenberger D, Kraševac Glaser A, Groonroos J, Hoffmann I, Hoffmann T, Hughes H, Ivanova M, Jezek P, Jones G, Ceren Karahan Z, Lass-Flörl C, Laurent F, Leach L, Horsbøll Pedersen ML, Loiez C, Lynch M, Maloney R, Marsh M, Milburn O, Mitchell S, Moore L, Moffat L, Murdjeva M, Murphy M, Nayar D, Nigrisoli G, O'Sullivan F, Öz B, Peach T, Petridou C, Prinz M, Rak M, Reidy N, Rossolini G, Roux AL, Ruiz-Garbajosa P, Saeed K, Salar-Vidal L, Salas Venero C, Selvaratnam M, Senneville E, Starzengruber P, Talbot B, Taylor V, Trebše R, Wearmouth D, Willinger B, Wouthuyzen-Bakker M, Couturier B, Allantaz F. Potential value of a rapid syndromic multiplex PCR for the diagnosis of native and prosthetic joint infections: a real-world evidence study. J Bone Jt Infect 2024; 9:87-97. [PMID: 38601005 PMCID: PMC11002912 DOI: 10.5194/jbji-9-87-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/01/2023] [Indexed: 04/12/2024] Open
Abstract
Introduction: The BIOFIRE Joint Infection (JI) Panel is a diagnostic tool that uses multiplex-PCR testing to detect microorganisms in synovial fluid specimens from patients suspected of having septic arthritis (SA) on native joints or prosthetic joint infections (PJIs). Methods: A study was conducted across 34 clinical sites in 19 European and Middle Eastern countries from March 2021 to June 2022 to assess the effectiveness of the BIOFIRE JI Panel. Results: A total of 1527 samples were collected from patients suspected of SA or PJI, with an overall agreement of 88.4 % and 85 % respectively between the JI Panel and synovial fluid cultures (SFCs). The JI Panel detected more positive samples and microorganisms than SFC, with a notable difference on Staphylococcus aureus, Streptococcus species, Enterococcus faecalis, Kingella kingae, Neisseria gonorrhoeae, and anaerobic bacteria. The study found that the BIOFIRE JI Panel has a high utility in the real-world clinical setting for suspected SA and PJI, providing diagnostic results in approximately 1 h. The user experience was positive, implying a potential benefit of rapidity of results' turnover in optimising patient management strategies. Conclusion: The study suggests that the BIOFIRE JI Panel could potentially optimise patient management and antimicrobial therapy, thus highlighting its importance in the clinical setting.
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Affiliation(s)
| | | | - Nusreen Ahmad-Saeed
- University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Catherine Aldridge
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom
| | - Simone Ambretti
- S. Orsola Bologna, Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Rachel Annett
- University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Shaan Ashk O'Shea
- University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Anna Maria Barbui
- San Giovanni Battista, Department of Public Health and Pediatrics Microbiology and Virology Unit, Città della Salute e della Scienza, Turin, Italy
| | - Gavin Barlow
- Hull University Teaching Hospitals NHS Trust, Hull, United Kingdom
| | | | | | - Alessandro Bondi
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - Nicola Boran
- Mater Misericordiae University Hospital, Dublin, Ireland
| | - Sara E. Boyd
- Chelsea and Westminster NHS Foundation Trust, London, United Kingdom
| | - Catarina Chaves
- Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | | | - Peter Davies
- NHS Greater Glasgow and Clyde, Glasgow Royal Infirmary, University of Glasgow, Glasgow, United Kingdom
| | - Ileana T. Dianzo-Delgado
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Jaime Esteban
- Dept. of Clinical Microbiology, IIS-Fundación Jiménez Díaz, CIBERINFEC-CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Stefan Fuchs
- Institute of Hygiene and Medical Microbiology Medizinische Universität Innsbruck, Innsbruck, Austria
| | - Lennart Friis-Hansen
- Copenhagen University Hospital, Bispebjerg, Copenhagen, Denmark
- Dept. Clinical Microbiology at Rigshospitalet, Copenhagen, Denmark
| | | | | | | | - Ines Hoffmann
- MVZ Labor Dr. Reising-Ackermann und Kollegen, Limbach Leipzig, Germany
| | | | - Harriet Hughes
- University Hospital of Wales, Cardiff, Wales, United Kingdom
| | | | - Peter Jezek
- Regional Hospital Příbram, Příbram, Czech Republic
| | - Gwennan Jones
- University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Zeynep Ceren Karahan
- Ankara University School of Medicine Department of Medical Microbiology, Ankara, Türkiye
| | - Cornelia Lass-Flörl
- Institute of Hygiene and Medical Microbiology Medizinische Universität Innsbruck, Innsbruck, Austria
| | | | - Laura Leach
- Oxford University Hospitals (OUH), Oxford, United Kingdom
| | - Matilde Lee Horsbøll Pedersen
- Copenhagen University Hospital, Bispebjerg, Copenhagen, Denmark
- Dept. Clinical Microbiology at Rigshospitalet, Copenhagen, Denmark
| | - Caroline Loiez
- Centre Hospitalier Universitaire de Lille, Lille, France
| | - Maureen Lynch
- Mater Misericordiae University Hospital, Dublin, Ireland
| | | | - Martin Marsh
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom
| | - Olivia Milburn
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom
| | | | - Luke S. P. Moore
- Chelsea and Westminster NHS Foundation Trust, London, United Kingdom
| | - Lynn Moffat
- NHS Greater Glasgow and Clyde, Glasgow Royal Infirmary, University of Glasgow, Glasgow, United Kingdom
| | | | - Michael E. Murphy
- NHS Greater Glasgow and Clyde, Glasgow Royal Infirmary, University of Glasgow, Glasgow, United Kingdom
| | - Deepa Nayar
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom
| | - Giacomo Nigrisoli
- S. Orsola Bologna, Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Büşra Öz
- Ankara University School of Medicine Department of Medical Microbiology, Ankara, Türkiye
| | - Teresa Peach
- University Hospital of Wales, Cardiff, Wales, United Kingdom
| | | | | | - Mitja Rak
- Koper lab, Orthopedic Hospital Valdoltra, Valdoltra, Slovenia
| | - Niamh Reidy
- Mater Misericordiae University Hospital, Dublin, Ireland
| | | | | | - Patricia Ruiz-Garbajosa
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III. Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Kordo Saeed
- University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Llanos Salar-Vidal
- Dept. of Clinical Microbiology, IIS-Fundación Jiménez Díaz, CIBERINFEC-CIBER de Enfermedades Infecciosas, Madrid, Spain
| | | | | | | | | | - Ben Talbot
- NHS Greater Glasgow and Clyde, Glasgow Royal Infirmary, University of Glasgow, Glasgow, United Kingdom
| | - Vanessa Taylor
- University Hospital of Wales, Cardiff, Wales, United Kingdom
| | - Rihard Trebše
- Koper lab, Orthopedic Hospital Valdoltra, Valdoltra, Slovenia
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Martin T, Martinot P, Leclerc JT, Titécat M, Loïez C, Dartus J, Duhamel A, Migaud H, Chantelot C, Lafon Desmurs B, Amouyel T, Senneville E. Accuracy of the GeneXpert® MRSA/SA SSTI test to diagnose methicillin-resistant Staphylococcus spp. infection in bone fixation and fusion and management of infected non-unions. Orthop Traumatol Surg Res 2024:103820. [PMID: 38266672 DOI: 10.1016/j.otsr.2024.103820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/22/2023] [Accepted: 10/16/2023] [Indexed: 01/26/2024]
Abstract
INTRODUCTION The GeneXpert® MRSA/SA SSTI (Methicillin Resistant Staphylococcus aureus/S. aureus skin and soft tissue infection) PCR test allows early detection of methicillin resistance in staphylococci. This test was developed for skin infections and has been evaluated for prosthetic joint infections but, to our knowledge, has not been evaluated for hardware infections outside of arthroplasties. Furthermore, we conducted a retrospective study in patients with non-prosthetic osteosynthesis hardware aiming: (1) to identify the diagnostic values of the PCR test compared to conventional cultures and the resulting rate of appropriate antibiotic therapy; (2) to identify the rate of false negative (FN) results; (3) to identify and compare the rates of failure of infectious treatment (FN versus others); (4) to search for risk factors for FN of the PCR test. HYPOTHESIS The PCR test allowed early and appropriate targeting of antibiotic therapy. MATERIAL AND METHODS The results of PCR tests and conventional cultures for osteoarticular infections of non-prosthetic hardware over four years (2012-2016) were compared to identify the diagnostic values of using the results of conventional culture as a reference and the rate of appropriate antibiotic therapies. Infectious management failures between the results of the FN group and the others were compared, and variables associated with a FN of the PCR test were identified. RESULTS The analysis of 419 PCR tests allowed us to establish a sensitivity of 42.86%, a specificity of 96.82%, a positive predictive value of 60% and a negative predictive value of 93.83%. Using the results of the PCR test for the targeting of postoperative antibiotic therapy, it was suitable for staphylococcal coverage in 90.94% (381/419). The rates of patients for whom infectious treatment failed were not significantly different between the FN group and the other patients (20.8% versus 17.7%, respectively; Hazard Ratio=1.12 (95%CI 0.47-2.69, p=0.79)). A skin opening during the initial trauma (p=0.005) and a polymicrobial infection were significantly associated with a risk of FN from the PCR test (p<0.001). CONCLUSION The PCR test makes it possible to reduce the duration of empirical broad-spectrum antibiotic therapy during the treatment of an infection of osteosynthesis hardware but causes a lack of antibiotic coverage in 9.06% of cases. LEVEL OF EVIDENCE III; diagnostic case control study.
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Affiliation(s)
- Théo Martin
- Service d'orthopédie, hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France.
| | - Pierre Martinot
- Département de chirurgie orthopédique, groupement des hôpitaux de l'institut catholique de Lille, université catholique de Lille, Lomme, France
| | - Jean-Thomas Leclerc
- Service d'orthopédie, hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Département de chirurgie orthopédique, CHU de Québec-université Laval, Quebec, Canada
| | - Marie Titécat
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Microbiologie, centre de biologie pathologie Pierre-Marie Degand, CHU de Lille, boulevard du Pr Jules-Leclercq, 59000 Lille, France
| | - Caroline Loïez
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Microbiologie, centre de biologie pathologie Pierre-Marie Degand, CHU de Lille, boulevard du Pr Jules-Leclercq, 59000 Lille, France
| | - Julien Dartus
- Service d'orthopédie, hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France
| | - Alain Duhamel
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre d'étude et de recherche en informatique médicale, maison de la recherche clinique hospitalière et universitaire, CHU de Lille, 6, rue du Professeur-Laguesse, 59000 Lille, France
| | - Henri Migaud
- Service d'orthopédie, hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France
| | - Christophe Chantelot
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Service de traumatologie, hôpital Salengro, CHU de Lille, place de Verdun, 59000 Lille, France
| | - Barthélémy Lafon Desmurs
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Service universitaire des maladies infectieuses, CH de Dron, 155, rue du Président-Coty, 59200 Tourcoing, France
| | - Thomas Amouyel
- Service d'orthopédie, hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France
| | - Eric Senneville
- CHU de Lille, Hôpital Salengro, University of Lille, Hauts-de-France, 59000, Lille, France; Centre de référence des infections ostéo-articulaires complexes Nord-Ouest (CRIOAC-NO), hôpital Salengro, CHU de Lille, place de Verdun, 59000, Lille, France; Service universitaire des maladies infectieuses, CH de Dron, 155, rue du Président-Coty, 59200 Tourcoing, France
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11
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Esteban J, Salar-Vidal L, Schmitt BH, Waggoner A, Laurent F, Abad L, Bauer TW, Mazariegos I, Balada-Llasat JM, Horn J, Wolk DM, Jefferis A, Hermans M, Verhoofstad I, Butler-Wu SM, Umali-Wilcox M, Murphy C, Cabrera B, Craft D, von Bredow B, Leber A, Everhart K, Dien Bard J, Flores II, Daly J, Barr R, Holmberg K, Graue C, Kensinger B. Multicenter evaluation of the BIOFIRE Joint Infection Panel for the detection of bacteria, yeast, and AMR genes in synovial fluid samples. J Clin Microbiol 2023; 61:e0035723. [PMID: 37877730 PMCID: PMC10662359 DOI: 10.1128/jcm.00357-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/07/2023] [Indexed: 10/26/2023] Open
Abstract
The bioMérieux BIOFIRE Joint Infection (JI) Panel is a multiplex in vitro diagnostic test for the simultaneous and rapid (~1 h) detection of 39 potential pathogens and antimicrobial resistance (AMR) genes directly from synovial fluid (SF) samples. Thirty-one species or groups of microorganisms are included in the kit, as well as several AMR genes. This study, performed to evaluate the BIOFIRE JI Panel for regulatory clearance, provides data from a multicenter evaluation of 1,544 prospectively collected residual SF samples with performance compared to standard-of-care (SOC) culture for organisms or polymerase chain reaction (PCR) and sequencing for AMR genes. The BIOFIRE JI Panel demonstrated a sensitivity of 90.9% or greater for all but six organisms and a positive percent agreement (PPA) of 100% for all AMR genes. The BIOFIRE JI Panel demonstrated a specificity of 98.5% or greater for detection of all organisms and a negative percent agreement (NPA) of 95.7% or greater for all AMR genes. The BIOFIRE JI Panel provides an improvement over SOC culture, with a substantially shorter time to result for both organisms and AMR genes with excellent sensitivity/PPA and specificity/NPA, and is anticipated to provide timely and actionable diagnostic information for joint infections in a variety of clinical scenarios.
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Affiliation(s)
- Jaime Esteban
- IIS-Fundacion Jimenez Diaz, CIBERINFEC-CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Llanos Salar-Vidal
- IIS-Fundacion Jimenez Diaz, CIBERINFEC-CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Bryan H. Schmitt
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Amy Waggoner
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | | | | | | | | | - Jared Horn
- The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | | | | | | | | | | | | | - Caitlin Murphy
- University of Nebraska Medical Center Omaha, Omaha, Nebraska, USA
| | - Barbara Cabrera
- University of Nebraska Medical Center Omaha, Omaha, Nebraska, USA
| | - David Craft
- The Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | | | - Amy Leber
- Nationwide Children’s Hospital, Columbus, Ohio, USA
| | | | | | | | - Judy Daly
- Primary Children’s Hospital, Salt Lake City, Utah, USA
| | - Rebecca Barr
- Primary Children’s Hospital, Salt Lake City, Utah, USA
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12
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Rimoldi SG, Brioschi D, Curreli D, Salari F, Pagani C, Tamoni A, Longobardi C, Bosari R, Rizzo A, Landonio S, Coen M, Passerini M, Gismondo MR, Gori A, Manzotti A. Traditional Cultures versus Next Generation Sequencing for Suspected Orthopedic Infection: Experience Gained from a Reference Centre. Antibiotics (Basel) 2023; 12:1588. [PMID: 37998790 PMCID: PMC10668678 DOI: 10.3390/antibiotics12111588] [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: 10/15/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
(Background) The diagnosis and the antimicrobial treatment of orthopedic infection are challenging, especially in cases with culture-negative results. New molecular methods, such as next-generation sequencing (NGS), promise to overcome some limitations of the standard culture, such as the detection of difficult-to-grow bacteria. However, data are scarce regarding the impact of molecular techniques in real-life scenarios. (Methods) We included cases of suspected orthopedic infection treated with surgery from May 2021 to September 2023. We combined traditional cultures with NGS. For NGS, we performed a metagenomic analysis of ribosomal 16s, and we queried dedicated taxonomic libraries to identify the species. To avoid false positive results, we set a cut-off of 1000 counts of the percentage of frequency of reads. (Results) We included 49 patients in our study. Our results show the presence of bacteria in 36/49 (73%) and 29/49 (59%) cases studied with NGS and traditional cultures, respectively. The concordance rate was 61%. Among the 19/49 discordant cases, in 11/19 cases, cultures were negative and NGS positive; in 4/19, cultures were positive and NGS negative; and in the remaining 4/19, different species were detected by traditional cultures and NGS. (Conclusions) Difficult-to-grow microorganisms, such as slow-growing anaerobic bacteria, were better detected by NGS compared to traditional culture in our study. However, more data to distinguish between true pathogens and contaminants are needed. NGS can be an additional tool to be used for the diagnosis of orthopedic infections and the choice of appropriate antimicrobial therapy.
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Affiliation(s)
- Sara Giordana Rimoldi
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Davide Brioschi
- Orthopedic Unit, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy
| | - Daniele Curreli
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Federica Salari
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Cristina Pagani
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Alessandro Tamoni
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Concetta Longobardi
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Raffaella Bosari
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Alberto Rizzo
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Simona Landonio
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy (M.C.)
| | - Massimo Coen
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy (M.C.)
| | - Matteo Passerini
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy (M.C.)
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza n. 35, 20122 Milan, Italy
| | - Maria Rita Gismondo
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy; (S.G.R.)
| | - Andrea Gori
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy (M.C.)
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza n. 35, 20122 Milan, Italy
- Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Via Francesco Sforza n. 35, 20122 Milan, Italy
| | - Alfonso Manzotti
- Orthopedic Unit, ASST Fatebenefratelli Sacco, “L. Sacco” University Hospital, Via Giovanni Battista Grassi n. 74, 20157 Milan, Italy
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13
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Poulsen SH, Søgaard KK, Fuursted K, Nielsen HL. Evaluating the diagnostic accuracy and clinical utility of 16S and 18S rRNA gene targeted next-generation sequencing based on five years of clinical experience. Infect Dis (Lond) 2023; 55:767-775. [PMID: 37535652 DOI: 10.1080/23744235.2023.2241550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND The use of 16S/18S rRNA targeted next-generation sequencing (tNGS) has improved microbial diagnostics, however, the use of tNGS in a routine clinical setting requires further elucidation. We retrospectively evaluated the diagnostic accuracy and clinical utility of 16S/18S tNGS, routinely used in the North Denmark Region between 2017 and 2021. METHODS We retrieved 544 tNGS results from 491 patients hospitalised with suspected infection (e.g. meningitis, pneumonia, intraabdominal abscess, osteomyelitis and joint infection). The tNGS assays was performed using the Illumina MiSeq desktop sequencer, and BION software for annotation. The patients' diagnosis and clinical management was evaluated by medical chart review. We calculated sensitivity and specificity, and determined the diagnostic accuracy of tNGS by defining results as true positive, true negative, false positive, and false negative. RESULTS Overall, tNGS had a sensitivity of 56% and a specificity of 97%. tNGS was more frequently true positive compared to culture (32% vs 18%), and tNGS detected a greater variety of bacteria and fungi, and was more frequently polymicrobial. However, the total diagnostic turnaround time was 16 days, and although 73% of tNGS results were true positive or true negative, only 4.4% of results led to changes in clinical management. CONCLUSIONS As a supplement to culture, tNGS improves identification of pathogenic microorganisms in a broad range of clinical specimens. However, the long turnaround time of tNGS in our setting may have contributed to a limited clinical utility. An improved turnaround time can be the key to improved clinical utility in a future setting.
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Affiliation(s)
| | - Kirstine Kobberøe Søgaard
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Hans Linde Nielsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
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14
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Berinson B, Spenke L, Krivec L, Tanida K, Both A, Keller J, Rolvien T, Christner M, Lütgehetmann M, Aepfelbacher M, Klatte TO, Rohde H. Performance and Hypothetical Impact on Joint Infection Management of the BioFire Joint Infection Panel: a Retrospective Analysis. J Clin Microbiol 2023; 61:e0059223. [PMID: 37439678 PMCID: PMC10446873 DOI: 10.1128/jcm.00592-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
Pathogen identification is key in septic arthritis. Culture-based techniques are challenging, especially when patients have been pretreated with antibiotics or when difficult-to-culture bacteria are encountered. The BioFire joint infection assay (BJA) is a multiplex PCR panel which detects 31 of the most prevalent bacterial and fungal pathogens causing septic arthritis. Here, 123 cryoconserved contemporary synovial fluid samples from 120 patients underwent BJA analysis. Results were compared to those of culture-based diagnostics (standard of care [SOC]). Clinical data were collected, and the possible impact of the molecular diagnostic application on patient management was evaluated. Fifteen of 123 synovial fluid cultures grew bacterial pathogens. All on-panel pathogens (9/15) were correctly identified by the BJA. The BJA identified four additional bacterial pathogens in four SOC-negative cases. BJA sensitivity and specificity were 100% (95% confidence interval [CI], 69.2% to 100%) and 100% (95% CI, 96.8% to 100%), respectively. Compared to the SOC, the BJA would have resulted in faster provision of species identification and molecular susceptibility data by 49 h and 99 h, respectively. Clinical data analysis indicates that in BJA-positive cases, faster species ID could have led to timelier optimization of antibiotic therapy. This retrospective study demonstrates high sensitivity and specificity of the BJA to detect on-panel organisms in bacterial arthritis. The usefulness of the BJA in prosthetic-joint infections is limited, as important pathogens (i.e., coagulase negative staphylococci and Cutibacterium acnes) are not covered. Evidence from patient data analysis suggests that the assay might prove valuable for optimizing patient management in acute arthritis related to fastidious organisms or for patients who received antibiotics prior to specimen collection.
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Affiliation(s)
- Benjamin Berinson
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Spenke
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lukas Krivec
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Konstantin Tanida
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Both
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johannes Keller
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Rolvien
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Christner
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Lütgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Orla Klatte
- Department of Trauma and Orthopaedic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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15
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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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Fisher CR, Patel R. Profiling the Immune Response to Periprosthetic Joint Infection and Non-Infectious Arthroplasty Failure. Antibiotics (Basel) 2023; 12:antibiotics12020296. [PMID: 36830206 PMCID: PMC9951934 DOI: 10.3390/antibiotics12020296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Arthroplasty failure is a major complication of joint replacement surgery. It can be caused by periprosthetic joint infection (PJI) or non-infectious etiologies, and often requires surgical intervention and (in select scenarios) resection and reimplantation of implanted devices. Fast and accurate diagnosis of PJI and non-infectious arthroplasty failure (NIAF) is critical to direct medical and surgical treatment; differentiation of PJI from NIAF may, however, be unclear in some cases. Traditional culture, nucleic acid amplification tests, metagenomic, and metatranscriptomic techniques for microbial detection have had success in differentiating the two entities, although microbiologically negative apparent PJI remains a challenge. Single host biomarkers or, alternatively, more advanced immune response profiling-based approaches may be applied to differentiate PJI from NIAF, overcoming limitations of microbial-based detection methods and possibly, especially with newer approaches, augmenting them. In this review, current approaches to arthroplasty failure diagnosis are briefly overviewed, followed by a review of host-based approaches for differentiation of PJI from NIAF, including exciting futuristic combinational multi-omics methodologies that may both detect pathogens and assess biological responses, illuminating causes of arthroplasty failure.
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Affiliation(s)
- Cody R. Fisher
- Mayo Clinic Graduate School of Biomedical Sciences, Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence:
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Affiliation(s)
- Robin Patel
- From the Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, and the Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, MN
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