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Jeyaraman M, Jeyaraman N, Nallakumarasamy A, Ramasubramanian S, Muthu S. Next Generation Sequencing in orthopaedic infections - Where is the road headed? J Clin Orthop Trauma 2024; 51:102397. [PMID: 38585384 PMCID: PMC10998229 DOI: 10.1016/j.jcot.2024.102397] [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: 01/18/2024] [Revised: 02/23/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Next-generation sequencing (NGS) has emerged as a game changer in the field of orthopaedic diagnostics, notably in the detection and management of infections associated with prosthetic joints and implants. This paper conducts an exhaustive examination of the pivotal role, outcomes, and prospective future uses of NGS in diagnosing orthopaedic infections. In comparison to conventional culture-based methods, NGS offers a marked improvement in sensitivity thereby facilitating prompt and comprehensive identification of pathogens. This encompasses the ability to detect polymicrobial infections, antibiotic-resistant strains, and previously imperceptible microorganisms. Furthermore, this article delves into the technology's contribution to advancing personalized medicine and promoting judicious antibiotic use. Nonetheless, the seamless integration of NGS into routine clinical practice is impeded by challenges such as substantial financial outlays, the requisite for specialized equipment and expertise, and the intricacy associated with data analysis. Notwithstanding these impediments, the potential for NGS to revolutionize orthopaedic diagnostics remains substantial, with ongoing advancements poised to address current limitations and broaden its scope within clinical applications.
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Affiliation(s)
- Madhan Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai, 600077, Tamil Nadu, India
- Orthopaedic Research Group, Coimbatore, 641045, Tamil Nadu, India
- Virginia Tech India, Chennai, 600095, Tamil Nadu, India
| | - Naveen Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai, 600077, Tamil Nadu, India
| | - Arulkumar Nallakumarasamy
- Department of Orthopaedics, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Karaikal, 609602, Puducherry, India
| | - Swaminathan Ramasubramanian
- Department of Orthopaedics, Government Medical College, Omandurar Government Estate, Chennai, 600002, Tamil Nadu, India
| | - Sathish Muthu
- Orthopaedic Research Group, Coimbatore, 641045, Tamil Nadu, India
- Department of Orthopaedics, Government Medical College and Hospital, Karur, 639004, Tamil Nadu, India
- Department of Biotechnology, Faculty of Engineering, Karpagam Academy of Higher Education, Coimbatore, 641021, Tamil Nadu, India
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Bureau A, Bourget-Murray J, Azad MA, Abdelbary H, Grammatopoulos G, Garceau SP. Management of Periprosthetic Joint Infections After Hemiarthroplasty of the Hip: A Critical Analysis Review. JBJS Rev 2022; 10:01874474-202209000-00006. [PMID: 36155552 DOI: 10.2106/jbjs.rvw.22.00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
➢ Periprosthetic joint infection (PJI) following hip hemiarthroplasty (HA) is a devastating complication, incurring immense health-care costs associated with its treatment and placing considerable burden on patients and their families. These patients often require multiple surgical procedures, extended hospitalization, and prolonged antimicrobial therapy. ➢ Notable risk factors include older age, higher American Society of Anesthesiologists (ASA) score, inadequate antibiotic prophylaxis, non-antibiotic-loaded cementation of the femoral implant, longer duration of the surgical procedure, and postoperative drainage and hematoma. ➢ Although the most frequent infecting organisms are gram-positive cocci such as Staphylococcus aureus, there is a higher proportion of patients with gram-negative and polymicrobial infections after hip HA compared with patients who underwent total hip arthroplasty. ➢ Several surgical strategies exist. Regardless of the preferred surgical treatment, successful management of these infections requires a comprehensive surgical debridement focused on eradicating the biofilm followed by appropriate antibiotic therapy. ➢ A multidisciplinary approach led by surgeons familiar with PJI treatment and infectious disease specialists is recommended for all cases of PJI after hip HA to increase the likelihood of treatment success.
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Affiliation(s)
- Antoine Bureau
- Division of Orthopaedic Surgery, The Ottawa Hospital, Ottawa, Ontario, Canada
| | | | - Marisa A Azad
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Hesham Abdelbary
- Division of Orthopaedic Surgery, The Ottawa Hospital, Ottawa, Ontario, Canada
| | | | - Simon P Garceau
- Division of Orthopaedic Surgery, The Ottawa Hospital, Ottawa, Ontario, Canada
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Genomics of Staphylococcus aureus and Staphylococcus epidermidis from Periprosthetic Joint Infections and Correlation to Clinical Outcome. Microbiol Spectr 2022; 10:e0218121. [PMID: 35762769 PMCID: PMC9430453 DOI: 10.1128/spectrum.02181-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The approach of sequencing or genotyping to characterize the pathogenic potential of staphylococci from orthopedic device-related infection (ODRI) has been applied in recent studies. These studies described the genomic carriage of virulence in clinical strains and compared it with those in commensal strains. Only a few studies have directly correlated genomic profiles to patient outcome and phenotypic virulence properties in periprosthetic joint infections (PJIs). We investigated the association between genomic variations and virulence-associated phenotypes (biofilm-forming ability and antimicrobial resistance) in 111 staphylococcal strains isolated from patients with PJI and the infection outcome (resolved/unresolved). The presence of a strong biofilm phenotype in Staphylococcus aureus and an antibiotic-resistant phenotype in Staphylococcus epidermidis were both associated with treatment failure of PJI. In S. epidermidis, multidrug resistance (MDR) and resistance to rifampicin were associated with unresolved infection. Sequence type 45 (ST45) and ST2 were particularly enriched in S. aureus and S. epidermidis, respectively. S. epidermidis ST2 caused the majority of relapses and was associated with MDR and strong biofilm production, whereas ST215 correlated with MDR and non/weak biofilm production. S. aureusagr II correlated with resolved infection, while S. epidermidisagr I was associated with strong biofilm production and agr III with non/weak production. Collectively, our results highlight the importance of careful genomic and phenotypic characterization to anticipate the probability of the strain causing treatment failure in PJI. Due to the high rate of resistant S. epidermidis strains identified, this study provides evidence that the current recommended treatment of rifampicin and a fluoroquinolone should not be administered without knowledge of the resistance pattern. IMPORTANCE This study addresses the presence and frequency of particular genetic variants and virulence factors found in staphylococcal bacteria causing periprosthetic joint infection (PJI) of the hip and knee to ascertain their clinical relevance as predictors of treatment failure. We characterized the genetic virulence traits of a large collection of clinical staphylococci isolated from patients with PJI and evaluated their association with the patient’s infection outcome. The results showed that S. aureus strains that produced strong biofilms and S. epidermidis strains with resistance to several antibiotics associated significantly with unresolved infection. Some particular genetic variants associated with biofilm formation and multidrug resistance. These traits should be considered important risk factors for the diagnosis and treatment guidance in PJI.
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Van Belkum A, Gros MF, Ferry T, Lustig S, Laurent F, Durand G, Jay C, Rochas O, Ginocchio CC. Novel strategies to diagnose prosthetic or native bone and joint infections. Expert Rev Anti Infect Ther 2021; 20:391-405. [PMID: 34384319 DOI: 10.1080/14787210.2021.1967745] [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] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Bone and Joint Infections (BJI) are medically important, costly and occur in native and prosthetic joints. Arthroplasties will increase significantly in absolute numbers over time as well as the incidence of Prosthetic Joint Infections (PJI). Diagnosis of BJI and PJI is sub-optimal. The available diagnostic tests have variable effectiveness, are often below standard in sensitivity and/or specificity, and carry significant contamination risks during the collection of clinical samples. Improvement of diagnostics is urgently needed. AREAS COVERED We provide a narrative review on current and future diagnostic microbiology technologies. Pathogen identification, antibiotic resistance detection, and assessment of the epidemiology of infections via bacterial typing are considered useful for improved patient management. We confirm the continuing importance of culture methods and successful introduction of molecular, mass spectrometry-mediated and next-generation genome sequencing technologies. The diagnostic algorithms for BJI must be better defined, especially in the context of diversity of both disease phenotypes and clinical specimens rendered available. EXPERT OPINION Whether interventions in BJI or PJI are surgical or chemo-therapeutic (antibiotics and bacteriophages included), prior sensitive and specific pathogen detection remains a therapy-substantiating necessity. Innovative tests for earlier and more sensitive and specific detection of bacterial pathogens in BJI are urgently needed.
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Affiliation(s)
- Alex Van Belkum
- bioMérieux, Open Innovation and Partnerships, 3 Route De Port Michaud, La Balme Les Grottes, France
| | | | - Tristan Ferry
- Service Des Maladies Infectieuses Et Tropicales, Hospices Civils De Lyon, Hôpital De La Croix-Rousse, Lyon, France.,Maladies Infectieuses, Université Claude Bernard Lyon 1, Villeurbanne, France.,Centre Interrégional De Référence Pour La Prise En Charge Des Infections Ostéo-articulaires Complexes (Crioac Lyon), Hôpital De La Croix-Rousse, Lyon, France.,Ciri - Centre International De Recherche En Infectiologie, Inserm, U1111, Université́ Claude Bernard Lyon 1CNRS, UMR5308, Ecole Normale Supérieure De Lyon, Univ Lyon, Lyon, France
| | - Sebastien Lustig
- Maladies Infectieuses, Université Claude Bernard Lyon 1, Villeurbanne, France.,Service De Chirurgie Orthopédique, Hôpital De La Croix-Rousse, Lyon, France
| | - Frédéric Laurent
- Service Des Maladies Infectieuses Et Tropicales, Hospices Civils De Lyon, Hôpital De La Croix-Rousse, Lyon, France.,Ciri - Centre International De Recherche En Infectiologie, Inserm, U1111, Université́ Claude Bernard Lyon 1CNRS, UMR5308, Ecole Normale Supérieure De Lyon, Univ Lyon, Lyon, France
| | | | - Corinne Jay
- bioMérieux, BioFire Development Emea, Grenoble, France
| | - Olivier Rochas
- Corporate Business Development, bioMérieux, Marcy-l'Étoile, France
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Ferreira FA, Helmersen K, Visnovska T, Jørgensen SB, Aamot HV. Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation. Microb Genom 2021; 7:000557. [PMID: 33885360 PMCID: PMC8208686 DOI: 10.1099/mgen.0.000557] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/13/2021] [Indexed: 01/18/2023] Open
Abstract
Outbreak investigations are essential to control and prevent the dissemination of pathogens. This study developed and validated a complete analysis protocol for faster and more accurate surveillance and outbreak investigations of antibiotic-resistant microbes based on Oxford Nanopore Technologies (ONT) DNA whole-genome sequencing. The protocol was developed using 42 methicillin-resistant Staphylococcus aureus (MRSA) isolates identified from former well-characterized outbreaks. The validation of the protocol was performed using Illumina technology (MiSeq, Illumina). Additionally, a real-time outbreak investigation of six clinical S. aureus isolates was conducted to test the ONT-based protocol. The suggested protocol includes: (1) a 20 h sequencing run; (2) identification of the sequence type (ST); (3) de novo genome assembly; (4) polishing of the draft genomes; and (5) phylogenetic analysis based on SNPs. After the sequencing run, it was possible to identify the ST in 2 h (20 min per isolate). Assemblies were achieved after 4 h (40 min per isolate) while the polishing was carried out in 7 min per isolate (42 min in total). The phylogenetic analysis took 0.6 h to confirm an outbreak. Overall, the developed protocol was able to at least discard an outbreak in 27 h (mean) after the bacterial identification and less than 33 h to confirm it. All these estimated times were calculated considering the average time for six MRSA isolates per sequencing run. During the real-time S. aureus outbreak investigation, the protocol was able to identify two outbreaks in less than 31 h. The suggested protocol enables identification of outbreaks in early stages using a portable and low-cost device along with a streamlined downstream analysis, therefore having the potential to be incorporated in routine surveillance analysis workflows. In addition, further analysis may include identification of virulence and antibiotic resistance genes for improved pathogen characterization.
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Affiliation(s)
- Fabienne Antunes Ferreira
- Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Karin Helmersen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology (Epigen), Akershus University Hospital and University of Oslo, Lørenskog, Norway
| | - Tina Visnovska
- Bioinformatics Core Facility, Oslo University Hospital Radium, Oslo, Norway
| | - Silje Bakken Jørgensen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Hege Vangstein Aamot
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
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