Shotgun-Metagenomics on Positive Blood Culture Bottles Inoculated With Prosthetic Joint Tissue: A Proof of Concept Study

Sanabria, Adriana Maria; Hjerde, Erik; Johannessen, Mona; Sollid, Johanna U. Ericson; Simonsen, Gunnar Skov; Hanssen, Anne-Merethe

doi:10.3389/fmicb.2020.01687

Cited by 11 publications

(17 citation statements)

References 82 publications

(138 reference statements)

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“…As identification of microorganisms in periprosthetic tissue samples is enhanced through molecular biology techniques, despite potential low bacterial load, different techniques are progressing towards higher sensitivity and specificity. Intraoperative samples inoculated in blood culture bottles allowed an increased identification of bacterial reads, 74 although the need for a positive blood culture may slow the diagnosis. Of considerable interest is the clinically relevant preoperative diagnosis.…”

Section: Implementing New Diagnostic Techniques In Clinical Practicementioning

confidence: 99%

An update about molecular biology techniques to detect orthopaedic implant-related infections

Esteban

Gómez‐Barrena

2021

EFORT Open Reviews

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Despite different criteria to diagnose a prosthetic joint infection (PJI), aetiological diagnosis of the causing microorganism remains essential to guide treatment. Molecular-biology-based PJI diagnosis is progressing (faster, higher specificity) in different techniques, from the experimental laboratory into clinical use. Multiplex polymerase chain reaction techniques (custom-made or commercial) provide satisfactory results in clinical series of cases, with specificity close to 100% and sensitivity over 70–80%. Next-generation metagenomics may increase sensitivity while maintaining high specificity. Molecular biology techniques may represent, in the next five years, a significant transformation of the currently available microbiological diagnosis in PJI. Cite this article: EFORT Open Rev 2021;6:93-100. DOI: 10.1302/2058-5241.6.200118

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Section: Implementing New Diagnostic Techniques In Clinical Practicementioning

confidence: 99%

An update about molecular biology techniques to detect orthopaedic implant-related infections

Esteban

Gómez‐Barrena

2021

EFORT Open Reviews

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“…Nineteen positive BCBs inoculated with PJT from 17 individual patients with suspicion of PJI were used in this study. Clinical samples were selected on the basis of being positive for S. aureus by the BCB method 16 , either monomicrobial (n = 18) or polymicrobial (n = 1). Samples were collected continuously over a 28-month period (August 2017-December 2019).…”

Section: Sample Collectionmentioning

confidence: 99%

“…DNA was extracted and processed as previously described 16 . In short, all samples were pre-treated using MolYsis™ Basic5 kit (Molzym, Bremen, Germany) to deplete human and horse DNA before DNA extraction using the QIAamp BiOstic Bacteremia DNA Kit (Qiagen, Hilden, Germany).…”

Section: Dna Preparationmentioning

confidence: 99%

“…synovial uid 9,10 , sonication uid [11][12][13][14] and tissue 15 , mainly for the identi cation of pathogens. In a previous study, we showed that SMg performed directly on positive blood culture bottles (BCBs) inoculated with prosthetic joint tissue (PJT), is a convenient method to identify potential pathogens causing PJI 16 . However, beyond the identi cation of pathogens, SMg provides unlimited access to other clinically relevant genomic features such as antibiotic resistance, virulence genes pro les and strain-level typing 17,18 .…”

Section: Introductionmentioning

confidence: 99%

“…We previously showed that SMg on BCBs with PJT resulted in acceptable high number of bacterial reads, genome coverage and genome sequencing depth 16 . Here, we wanted to assess the potential of SMg for the identi cation and typing of the most common cause of PJI, S. aureus, and the prediction of virulence and AMR directly from clinical samples.…”

Section: Introductionmentioning

confidence: 99%

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Shotgun-Metagenomics Based Prediction Of Antibiotic Resistance And Virulence Determinants In Staphylococcus Aureus From Prosthetic Joint Tissue On Blood Culture Bottles

Sanabria

Janice

Hjerde

et al. 2021

Preprint

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Shotgun-metagenomics may give valuable clinical information beyond the detection of potential pathogen(s). Identification of antimicrobial resistance (AMR), virulence genes and typing directly from clinical samples has been limited due to challenges arising from incomplete genome coverage. We assessed the performance of shotgun-metagenomics on positive blood culture bottles (n = 19) with prosthetic joint tissue for typing and prediction of AMR and virulence profiles in Staphylococcus aureus. We used different approaches to determine if sequence data from reads provides more information than from assembled contigs. Only 0.18% of total reads was derived from human DNA. Shotgun-metagenomics results and conventional method results were consistent in detecting S. aureus in all samples. AMR and known prosthetic joint infection virulence genes were predicted from S. aureus. Mean coverage depth, when predicting AMR genes was 209x. Resistance phenotypes could be explained by genes predicted in the sample in most of the cases. The choice of bioinformatic data analysis had a significant impact on the results. Read-based analysis was more accurate for pathogen identification, while contigs seemed better for AMR profiling. Our study demonstrates high genome coverage and potential for typing and prediction of AMR and virulence profiles in S. aureus from shotgun-metagenomics data.

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Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics

Lee,

Ng,

Wong

et al. 2024

Food Microbiology

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Shotgun-Metagenomics on Positive Blood Culture Bottles Inoculated With Prosthetic Joint Tissue: A Proof of Concept Study

Cited by 11 publications

References 82 publications

An update about molecular biology techniques to detect orthopaedic implant-related infections

An update about molecular biology techniques to detect orthopaedic implant-related infections

Shotgun-Metagenomics Based Prediction Of Antibiotic Resistance And Virulence Determinants In Staphylococcus Aureus From Prosthetic Joint Tissue On Blood Culture Bottles

Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics

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