Evidence map›Paper›PMID 41665488›Full record

ArticleMicrobial genomics2026

Evaluation of Oxford Nanopore Technologies workflows for genomic epidemiology of outbreak-associated bacterial isolates in the clinical setting.

Stefan Neuenschwander, Loïc Borcard, Sonja Gempeler, Miguel A Terrazos Miani, Carlo Casanova, Alban Ramette

Abstract readEvaluation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbial genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Applicability of Nanopore-only whole-genome sequencing forJournal of clinical microbiology · 2026
    Article
  2. Article
  3. Article
  4. 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

6 authors.

Stefan NeuenschwanderInstitute for Infectious Diseases, University of Bern, Bern, Switzerland.
Loïc BorcardInstitute for Infectious Diseases, University of Bern, Bern, Switzerland.
Sonja GempelerInstitute for Infectious Diseases, University of Bern, Bern, Switzerland.
Miguel A Terrazos MianiInstitute for Infectious Diseases, University of Bern, Bern, Switzerland.
Carlo CasanovaInstitute for Infectious Diseases, University of Bern, Bern, Switzerland.
Alban RametteInstitute for Infectious Diseases, University of Bern, Bern, Switzerland.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Accurate and efficient whole-genome sequencing (WGS) is crucial for clinical diagnostics and surveillance of bacterial infections. Here, we investigate the potential of a new Oxford Nanopore Technologies (ONT) workflow for WGS of clinically relevant bacterial isolates. Specifically, we assess the performance of R10.4.1 flow cells in combination with the V14 version of the transposase-based (RBK) library preparation kit to provide rapid and accurate genomic epidemiological comparisons of bacterial species of clinical importance. We focused on retrospective collections of outbreak-associated

Indexed as

Bacterial InfectionsCorynebacterium diphtheriaeNanopore SequencingVancomycin-Resistant EnterococciWhole Genome SequencingDisease OutbreaksDrug Resistance, BacterialGenome, BacterialGenomicsHumansMolecular EpidemiologyMultilocus Sequence TypingPolymorphism, Single NucleotideWorkflowbacterial pathogensclinical settingcore-genome multi-locus sequence typing (cgMLST)genome assemblygenomic epidemiologyoutbreakOxford Nanopore TechnologiesplasmidsR10.4.1

Identifiers

PMID41665488
PMCPMC12890258

What OpenQuestion holds

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LicenceCC BY
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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.