ArticleJournal of clinical microbiology2022
Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopedic Device Infection.
Article in Journal of clinical microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
- The diagnostic potential of combined quantitative polymerase chain reaction and next-generation sequencing using the same primers for periprosthetic joint infection.Microbiology spectrum · 2026Article
- Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid pathogen and antimicrobial resistance detection.npj antimicrobials and resistance · 2026Review
- Current Concepts in Periprosthetic Joint Infection: Modern Biomarkers, Microbiome Insights, Molecular Diagnostics, and Emerging Prevention Strategies.Orthopedic research and reviews · 2026Review
- Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue.Microbial genomics · 2025Article
- China Expert consensus on the application of metagenomic next-generation sequencing for the etiological diagnosis of infections in hematological disorders (2024).Blood science (Baltimore, Md.) · 2025Article
- Article
- Detecting antibiotic resistance: classical, molecular, advanced bioengineering, and AI-enhanced approaches.Frontiers in microbiology · 2025Review
- Global trends in the application of nanopore sequencing technology in the detection of infectious disease pathogens: a bibliometric analysis from 2014 to 2024.Frontiers in medicine · 2025Article
- Routine Metagenomics Service for ICU Patients with Respiratory Infection.American journal of respiratory and critical care medicine · 2024Article
- Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana.Nature microbiology · 2023Article
- Composition of pathogenic microorganism in chronic osteomyelitis based on metagenomic sequencing and its application value in etiological diagnosis.BMC microbiology · 2023Article
- Rapid Diagnostics of Joint Infections Using IS-Pro.Journal of clinical microbiology · 2023Article
- Making the diagnosis in prosthetic joint infection: a European view.EFORT open reviews · 2023Review
- Direct Prosthetic Joint Infection Diagnosis from Sonication Fluid Inoculated in Blood Culture Bottles by Direct MALDI-TOF Mass Spectrometry.Diagnostics (Basel, Switzerland) · 2023Article
- Advances in the Microbiological Diagnosis of Prosthetic Joint Infections.Diagnostics (Basel, Switzerland) · 2023Review
- Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections withFrontiers in cellular and infection microbiology · 2023Article
- Application of nanopore adaptive sequencing in pathogen detection of a patient withFrontiers in cellular and infection microbiology · 2023Article
- Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications.Microbial genomics · 2022Article
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 2 countries.
Funding
Abstract
Diagnosis of orthopedic device-related infection is challenging, and causative pathogens may be difficult to culture. Metagenomic sequencing can diagnose infections without culture, but attempts to detect antimicrobial resistance (AMR) determinants using metagenomic data have been less successful. Human DNA depletion may maximize the amount of microbial DNA sequence data available for analysis. Human DNA depletion by saponin was tested in 115 sonication fluid samples generated following revision arthroplasty surgery, comprising 67 where pathogens were detected by culture and 48 culture-negative samples. Metagenomic sequencing was performed on the Oxford Nanopore Technologies GridION platform. Filtering thresholds for detection of true species versus contamination or taxonomic misclassification were determined. Mobile and chromosomal genetic AMR determinants were identified in Staphylococcus aureus-positive samples. Of 114 samples generating sequence data, species-level positive percent agreement between metagenomic sequencing and culture was 50/65 (77%; 95% confidence interval [CI], 65 to 86%) and negative percent agreement was 103/114 (90%; 95% CI, 83 to 95%). Saponin treatment reduced the proportion of human bases sequenced in comparison to 5-μm filtration from a median (interquartile range [IQR]) of 98.1% (87.0% to 99.9%) to 11.9% (0.4% to 67.0%), improving reference genome coverage at a 10-fold depth from 18.7% (0.30% to 85.7%) to 84.3% (12.9% to 93.8%). Metagenomic sequencing predicted 13/15 (87%) resistant and 74/74 (100%) susceptible phenotypes where sufficient data were available for analysis. Metagenomic nanopore sequencing coupled with human DNA depletion has the potential to detect AMR in addition to species detection in orthopedic device-related infection. Further work is required to develop pathogen-agnostic human DNA depletion methods, improving AMR determinant detection and allowing its application to other infection types.
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