Evidence map›Paper›PMID 24853639›Full record

ArticleNature communications2014

Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus.

Richard G Everitt, Xavier Didelot, Elizabeth M Batty, Ruth R Miller, Kyle Knox, Bernadette C Young, Rory Bowden, Adam Auton, Antonina Votintseva, Hanna Larner-Svensson and 9 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.

0numbers the graph read from it
0cells of the map it votes in
99citing papers in PubMed
8.1field-weighted citation impact, top 2% of its field
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

99 citing papers in PubMed, 164 citations in OpenAlex.

  1. Article
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  4. Linkage of nucleotide and functional diversity varies across gut bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2026
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  5. Review
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  7. Dynamics of dN/dS within recombining bacterial populations.bioRxiv : the preprint server for biology · 2025
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  9. Transition ofbioRxiv : the preprint server for biology · 2025
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39 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

19 authors at 4 institutions in 1 country.

Richard G Everitt1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2].
Xavier Didelot1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2].
Elizabeth M Batty1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Ruth R MillerNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Kyle KnoxDepartment of Primary Care Health Sciences, University of Oxford, 23-38 Hythe Bridge Street, Oxford OX1 2ET, UK.
Bernadette C YoungNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Rory Bowden1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Adam AutonWellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Antonina Votintseva1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.
Hanna Larner-Svensson1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Jane CharlesworthNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Tanya Golubchik1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.
Camilla L C Ip1] Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Heather GodwinOxford University Hospitals National Health Service Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Rowena FungNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Tim E A PetoNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
A Sarah WalkerNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Derrick W CrookNuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Daniel J Wilson1] Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK [2] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
John Radcliffe Hospital · GBUniversity of Oxford · GBCentre for Human Genetics · GBUniversity of Reading · GB

Funding

Department of Health G0800778Medical Research Council G0800778Medical Research Council MR/K010174/1Wellcome Trust 087646Wellcome Trust 087646/Z/08/ZWellcome Trust 090532/Z/09/ZWellcome Trust 101237Wellcome Trust 101237/Z/13/Z
6 · The paper itself

Abstract

Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange in the core genome of clonal species, including the major pathogen Staphylococcus aureus, is incompletely understood. Here we reveal widespread homologous recombination in S. aureus at the species level, in contrast to its near-complete absence between closely related strains. We discover a patchwork of hotspots and coldspots at fine scales falling against a backdrop of broad-scale trends in rate variation. Over megabases, homoplasy rates fluctuate 1.9-fold, peaking towards the origin-of-replication. Over kilobases, we find core recombination hotspots of up to 2.5-fold enrichment situated near fault lines in the genome associated with mobile elements. The strongest hotspots include regions flanking conjugative transposon ICE6013, the staphylococcal cassette chromosome (SCC) and genomic island νSaα. Mobile element-driven core genome transfer represents an opportunity for adaptation and challenges our understanding of the recombination landscape in predominantly clonal pathogens, with important implications for genotype-phenotype mapping.

Indexed as

Recombination, GeneticChromosomes, BacterialDNA Transposable ElementsGenetic VariationGene Transfer, HorizontalGenome, BacterialLikelihood FunctionsLinkage DisequilibriumPhylogenySpecies SpecificityStaphylococcus aureusDNA Transposable Elements

Identifiers

PMID24853639
PMCPMC4036114
OpenAlexW2091828194

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.