Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue.

Teresa L Street, Philip Bejon, Laura Leach, Sarah Oakley, Bernadette C Young, Nicholas D Sanderson

Abstract read

In one paragraph

Article in Microbial genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

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0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

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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

6 authors.

Teresa L StreetNIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.

Philip BejonModernising Medical Microbiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

Laura LeachOxford University Hospitals NHS Trust, Oxford, UK.

Sarah OakleyOxford University Hospitals NHS Trust, Oxford, UK.

Bernadette C YoungNIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.

Nicholas D SandersonNIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Metagenomic approaches to the diagnosis of prosthetic joint infections promise more accurate and more rapid diagnosis. However, the high host DNA to bacterial DNA ratio is a challenge. Nanopore adaptive sampling (AS) can be used to preferentially sequence more of the infecting organism. Here, we evaluate AS using clinical samples from infected prosthetic joints to determine the absolute fold enrichment achieved. We found that AS achieved a range of 1.61- to 1.96-fold higher absolute fold enrichment for bacterial sequenced bases using AS over control pores. In this limited sample set, AS did not impact bacterial diagnosis overall but led to a modest increase in the bacterial sequence available without any obvious cost.

Indexed as

BacteriaJoint ProsthesisMetagenomicsNanoporesProsthesis-Related InfectionsDNA, BacterialHumansDNA, Bacterialadaptive samplingclinical metagenomicsdiagnosticsdirect from sample sequencingnanopore

Identifiers

PMID40990924

DOI10.1099/mgen.0.001507

PMCPMC13293318

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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.