Evidence map›Paper›PMID 35143385›Full record

ArticleMicrobial genomics2022

Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in

Jonathan S Abrahams, Michael R Weigand, Natalie Ring, Iain MacArthur, Joss Etty, Scott Peng, Margaret M Williams, Barret Bready, Anthony P Catalano, Jennifer R Davis and 7 more

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

Article in Microbial genomics, 2022. 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
0.9field-weighted citation impact, top 30% 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

4 citing papers in PubMed, 7 citations in OpenAlex.

  1. Review
  2. mSystems · 2025
    Article
  3. A role for genomics-based studies of Bordetella pertussis adaptation.Current opinion in infectious diseases · 2025
    Review
  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

17 authors at 4 institutions in 2 countries.

Jonathan S AbrahamsDepartment of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK.
Michael R WeigandDivision of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Natalie RingDepartment of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK.
Iain MacArthurDepartment of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK.
Joss EttyDepartment of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK.
Scott PengDivision of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Margaret M WilliamsDivision of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Barret BreadyNabsys 2.0, Providence, RI 02809, USA.
Anthony P CatalanoNabsys 2.0, Providence, RI 02809, USA.
Jennifer R DavisNabsys 2.0, Providence, RI 02809, USA.
Michael D KaiserNabsys 2.0, Providence, RI 02809, USA.
John S OliverNabsys 2.0, Providence, RI 02809, USA.
Jay M SageNabsys 2.0, Providence, RI 02809, USA.
Stefan BagbyDepartment of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK.
M Lucia TondellaDivision of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Andrew R GorringePublic Health England, Porton Down, Salisbury, UK.
Andrew PrestonDepartment of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK.
Providence College · USUniversity of Bath · GBCenters for Disease Control and Prevention · USPublic Health England · GB

Funding

Medical Research Council MR/L015080/1
6 · The paper itself

Abstract

Bacterial genetic diversity is often described solely using base-pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplication/amplifications are thought to be widespread among bacteria but due to their often-intractable size and instability, comprehensive studies of these mutations are rare. We define a methodology to investigate amplifications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with

Indexed as

Genetic VariationBordetella pertussisGenes, BacterialGenome, BacterialGenomic InstabilityMutationMycobacterium tuberculosisPhylogenyVirulenceWhooping CoughamplificationsB. pertussisduplicationsgenetic diversitygenome structure

Identifiers

PMID35143385
PMCPMC8942028
OpenAlexW4210972198

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.