Preliminary assessment of nanopore-based metagenomic sequencing for the diagnosis of prosthetic joint infection

Wang, Chao‐xin; Huang, Zida; Wei, Fang; Zhang, Zijie; Fang, Xinyu; Li, Wenbo; Yang, Bin; Chen, Luyao; Liang, Xiangzhi; Hu, Huan; Shi, Duozhi; Lee, Shela; Zhang, Wenming

doi:10.1016/j.ijid.2020.05.044

Cited by 25 publications

(18 citation statements)

References 26 publications

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“…Wang at al. conducted a preliminary assessment of this technology (46). The authors were able to identify the causative microorganisms of PJI within approximately 12 hours after sample collection.…”

Section: Molecular Diagnostic Testsmentioning

confidence: 99%

“…The authors were able to identify the causative microorganisms of PJI within approximately 12 hours after sample collection. Furthermore, the detection of corresponding antimicrobial resistance determinants was faster compared to short-read based mNGS (46). NGS performed on cultured microorganisms isolated from a patient experiencing two episodes of PJI within a 9-month period was crucial to understand that the second episode was a new infection with the same bacterial species (47).…”

Section: Molecular Diagnostic Testsmentioning

confidence: 99%

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Precision Medicine in the Diagnosis and Management of Orthopedic Biofilm Infections

Baldan

Sendi

2020

Front. Med.

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Section: Molecular Diagnostic Testsmentioning

confidence: 99%

Section: Molecular Diagnostic Testsmentioning

confidence: 99%

Precision Medicine in the Diagnosis and Management of Orthopedic Biofilm Infections

Baldan

Sendi

2020

Front. Med.

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“… 60 This technology allows for real-time analysis while sequencing is ongoing, significantly reducing the turnaround time ( Table 2 ). Wang et al 61 compared the classic metagenomic NGS, nanopore-based metagenomic sequencing and classical culture for the diagnosis of prosthetic joint infections from collected joint fluid, periprosthetic tissue and sonication fluid. Interestingly, the two metagenomic methods showed a similar sensitivity rate but the nanopore-based metagenomic sequencing method showed a better specificity and a quicker turnaround time (14–22 hours).…”

Section: Introductionmentioning

confidence: 99%

Next generation sequencing for pathogen detection in periprosthetic joint infections

et al. 2021

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Periprosthetic joint infections (PJI) represent one of the most catastrophic complications following total joint arthroplasty (TJA). The lack of standardized diagnostic tests and protocols for PJI is a challenge for arthroplasty surgeons. Next generation sequencing (NGS) is an innovative diagnostic tool that can sequence microbial deoxyribonucleic acids (DNA) from a synovial fluid sample: all DNA present in a specimen is sequenced in parallel, generating millions of reads. It has been shown to be extremely useful in a culture-negative PJI setting. Metagenomic NGS (mNGS) allows for universal pathogen detection, regardless of microbe type, in a 24–48-hour timeframe: in its nanopore-base variation, mNGS also allows for antimicrobial resistance characterization. Cell-free DNA (cfDNA) NGS, characterized by lack of the cell lysis step, has a fast run-time (hours) and, together with a high sensitivity and specificity in microorganism isolation, may provide information on the presence of antimicrobial resistance genes. Metagenomics and cfDNA testing have reduced the time needed to detect infecting bacteria and represent very promising technologies for fast PJI diagnosis. NGS technologies are revolutionary methods that could disrupt the diagnostic paradigm of PJI, but a comprehensive collection of clinical evidence is still needed before they become widely used diagnostic tools. Cite this article: EFORT Open Rev 2021;6:236-244. DOI: 10.1302/2058-5241.6.200099

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“…Several studies [9][10][11][12][13][14][15] have shown metagenomic sequencing can identify causative pathogens in PJI, achieving species-level sensitivity of 83-96%, and potentially identifying difficult to grow organisms and pathogens following prior antibiotics. However, lack of comprehensive antimicrobial susceptibility prediction from orthopaedic metagenomic sequencing has limited its application.…”

Section: Introductionmentioning

confidence: 99%

Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopaedic Device Infection

Street

Sanderson

Kolenda

et al. 2021

Preprint

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Background Diagnosis of orthopaedic 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 maximise the amount of microbial DNA sequence data available for analysis. Methods 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. Results Of 114 samples generating sequence data, species-level sensitivity of metagenomic sequencing was 49/65 (75%; 95%CI 63-85%) and specificity 103/114 (90%; 95%CI 83-95%) compared with culture. Saponin treatment reduced the proportion of human bases sequenced in comparison to 5um filtration from a median (IQR) 98.1% (87.0%-99.9%) to 11.9% (0.4%-67.0%), improving reference genome coverage at 10-fold depth from 18.7% (0.30%-85.7%) to 84.3% (12.9%-93.8%). Metagenomic sequencing predicted 13/15 (87%) resistant and 74/74 (100%) susceptible phenotypes where sufficient data were available for analysis. Conclusions Metagenomic nanopore sequencing coupled with human DNA depletion has the potential to detect AMR in addition to species detection in orthopaedic 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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Preliminary assessment of nanopore-based metagenomic sequencing for the diagnosis of prosthetic joint infection

Cited by 25 publications

References 26 publications

Precision Medicine in the Diagnosis and Management of Orthopedic Biofilm Infections

Precision Medicine in the Diagnosis and Management of Orthopedic Biofilm Infections

Next generation sequencing for pathogen detection in periprosthetic joint infections

Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopaedic Device Infection

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