Evidence map›Paper›PMID 41396803›Full record

ArticleMicrobial genomics2025

Characterizing the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse test set of 2,663

Jeremy Westhead, Catriona S Baker, Marc Brouard, Matthew Colpus, Bede Constantinides, Alexandra Hall, Jeff Knaggs, Marcela Lopes Alves, Ruan Spies, Hieu Thai and 7 more

Abstract read
PubMed Full text at PMC Publisher
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. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
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

17 authors.

Jeremy WestheadNuffield Department of Medicine, University of Oxford, Oxford, UK.
Catriona S BakerNuffield Department of Medicine, University of Oxford, Oxford, UK.
Marc BrouardNuffield Department of Medicine, University of Oxford, Oxford, UK.
Matthew ColpusNuffield Department of Medicine, University of Oxford, Oxford, UK.
Bede ConstantinidesNuffield Department of Medicine, University of Oxford, Oxford, UK.
Alexandra HallNuffield Department of Medicine, University of Oxford, Oxford, UK.
Jeff KnaggsNuffield Department of Medicine, University of Oxford, Oxford, UK.
Marcela Lopes AlvesNuffield Department of Medicine, University of Oxford, Oxford, UK.
Ruan SpiesNuffield Department of Medicine, University of Oxford, Oxford, UK.
Hieu ThaiNuffield Department of Medicine, University of Oxford, Oxford, UK.
Sarah SurrallEllison Institute of Technology, Oxford Ltd, Oxford, UK.
Kumeren GovenderEllison Institute of Technology, Oxford Ltd, Oxford, UK.
Timothy E A PetoNuffield Department of Medicine, University of Oxford, Oxford, UK.
Derrick W CrookNuffield Department of Medicine, University of Oxford, Oxford, UK.
Shaheed V OmarCentre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, National, Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa.
Robert TurnerNuffield Department of Medicine, University of Oxford, Oxford, UK.
Philip W FowlerNuffield Department of Medicine, University of Oxford, Oxford, UK.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Tuberculosis remains a global health problem. Making it easier and quicker to identify which antibiotics an infection is likely to be susceptible to will be a key part of the solution. Whilst whole-genome sequencing offers many advantages, the processing of the genetic reads to produce the relevant public health and clinical information is, surprisingly, often the responsibility of the end user, which inhibits uptake. Here, we characterize how well a freely available tool we have developed, gnomonicus, predicts the antibiotic resistance profile of a sample (given its variant call file) using our implementation of the second edition of the World Health Organization (WHO) catalogue of resistance-associated variants (WHOv2). To facilitate this, we have constructed a diverse test set of 2,663 publicly available

Indexed as

Drug Resistance, BacterialMycobacterium tuberculosisAntitubercular AgentsGenome, BacterialHumansMicrobial Sensitivity TestsTuberculosisWhole Genome SequencingAntitubercular Agentsantimicrobial resistancediagnosticstuberculosis (TB)whole-genome sequencing (WGS)

Identifiers

PMID41396803
PMCPMC12705075

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.