Evidence map›Paper›PMID 29648630›Full record

ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2018

Identification of Prosthetic Joint Infection Pathogens Using a Shotgun Metagenomics Approach.

Matthew J Thoendel, Patricio R Jeraldo, Kerryl E Greenwood-Quaintance, Janet Z Yao, Nicholas Chia, Arlen D Hanssen, Matthew P Abdel, Robin Patel

Registry-linked trialAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT04864873 (An External Evaluation of a Metagenomic Next Generation Sequencing Workflow for Infection Diagnosis Using Oxford Nanopore Sequencing.), which is not on this map. Cited by 132 papers, 8 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
132citing papers in PubMed, 8 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

NCT04864873 naunknown statusnot on this mapstarted 2021, after this paper: background citation

An External Evaluation of a Metagenomic Next Generation Sequencing Workflow for Infection Diagnosis Using Oxford Nanopore Sequencing.

TypeinterventionalSponsorCapital and Coast District Health boardRan2021 to 2022Enrolled400ConditionsBacterial InfectionsArmsMetagenomic next generation sequencing using Oxford Nanopore, Standard microbiological diagnostic pathway
3 · Its place in the literature

Who cites it

132 citing papers in PubMed, 8 syntheses or guidelines pooled it.

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  12. Diagnostic accuracy and clinical considerations of metagenomic next-generation sequencing in prosthetic joint infection: a systematic review and meta-analysis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026
    Review
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  18. Identification of miRNA Biomarkers Associated With Staphylococcal Musculoskeletal Infections.Journal of orthopaedic research : official publication of the Orthopaedic Research Society · 2025
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72 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Matthew J ThoendelDivision of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota.
Patricio R JeraldoDepartment of Surgery, Mayo Clinic, Rochester, Minnesota.
Kerryl E Greenwood-QuaintanceDivision of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
Janet Z YaoDepartment of Surgery, Mayo Clinic, Rochester, Minnesota.
Nicholas ChiaDepartment of Surgery, Mayo Clinic, Rochester, Minnesota.
Arlen D HanssenDepartment of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota.
Matthew P AbdelDepartment of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota.
Robin PatelDivision of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota.

Funding

Molecular Detection of Biofilms on Hip and Knee ImplantsR01AR056647 · NIAMS · MAYO CLINIC ROCHESTER · PI PATEL, ROBIN · 2009 to 2020
$4.5M
Microbial Metabolic Toxicity Drives Colon CancerR01CA179243 · NCI · MAYO CLINIC ROCHESTER · PI CHIA, NICHOLAS · 2014 to 2018
$2.0M
NCI NIH HHS R01 CA179243NIAMS NIH HHS R01 AR056647
6 · The paper itself

Abstract

Background: Metagenomic shotgun sequencing has the potential to change how many infections, particularly those caused by difficult-to-culture organisms, are diagnosed. Metagenomics was used to investigate prosthetic joint infections (PJIs), where pathogen detection can be challenging. Methods: Four hundred eight sonicate fluid samples generated from resected hip and knee arthroplasties were tested, including 213 from subjects with infections and 195 from subjects without infection. Samples were enriched for microbial DNA using the MolYsis basic kit, whole-genome amplified, and sequenced using Illumina HiSeq 2500 instruments. A pipeline was designed to screen out human reads and analyze remaining sequences for microbial content using the Livermore Metagenomics Analysis Toolkit and MetaPhlAn2 tools. Results: When compared to sonicate fluid culture, metagenomics was able to identify known pathogens in 94.8% (109/115) of culture-positive PJIs, with additional potential pathogens detected in 9.6% (11/115). New potential pathogens were detected in 43.9% (43/98) of culture-negative PJIs, 21 of which had no other positive culture sources from which these microorganisms had been detected. Detection of microorganisms in samples from uninfected aseptic failure cases was conversely rare (7/195 [3.6%] cases). The presence of human and contaminant microbial DNA from reagents was a challenge, as previously reported. Conclusions: Metagenomic shotgun sequencing is a powerful tool to identify a wide range of PJI pathogens, including difficult-to-detect pathogens in culture-negative infections.

Indexed as

MetagenomicsProsthesis FailureAdolescentAdultAgedAged, 80 and overArthroplasty, Replacement, HipArthroplasty, Replacement, KneeBacteriaFemaleHigh-Throughput Nucleotide SequencingHumansMaleMicrobiological TechniquesMiddle AgedProsthesis-Related Infections

Identifiers

PMID29648630
PMCPMC6186856

What OpenQuestion holds

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Registered trials

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.