Evidence map›Paper›PMID 39994515›Full record

ArticleBMC genomics2025

Lineage-specific variation in frequency and hotspots of recombination in invasive Escherichia coli.

Kathryn R Piper, Stephanie S R Souza, Odion O Ikhimiukor, Adrienne A Workman, Isabella W Martin, Cheryl P Andam

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In one paragraph

Article in BMC 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

6 authors.

Kathryn R PiperDepartment of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.ORCID http://orcid.org/0000-0003-2711-2347
Stephanie S R SouzaDepartment of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.ORCID http://orcid.org/0000-0002-4207-8231
Odion O IkhimiukorDepartment of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.ORCID http://orcid.org/0000-0002-3738-4584
Adrienne A WorkmanDepartment of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA.
Isabella W MartinDepartment of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA. isabella.w.martin@hitchcock.org.ORCID http://orcid.org/0000-0001-7974-9767
Cheryl P AndamDepartment of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA. candam@albany.edu.ORCID http://orcid.org/0000-0003-4428-0924

Funding

Population and evolutionary dynamics of recombining genes and alleles in bacteriaR35GM142924 · NIGMS · STATE UNIVERSITY OF NEW YORK AT ALBANY · PI Cheryl Marie P Andam · 2021 to 2026
$1.9M
NIGMS NIH HHS R35 GM142924NIH HHS R35GM142924
6 · The paper itself

Abstract

backgroundThe opportunistic bacterium Escherichia coli can invade normally sterile sites in the human body, potentially leading to life-threatening organ dysfunction and even death. However, our understanding of the evolutionary processes that shape its genetic diversity in this sterile environment remains limited. Here, we aim to quantify the frequency and characteristics of homologous recombination in E. coli from bloodstream infections.

resultsAnalysis of 557 short-read genome sequences revealed that the propensity to exchange DNA by homologous recombination varies within a distinct population (bloodstream) at narrow geographic (Dartmouth Hitchcock Medical Center, New Hampshire, USA) and temporal (years 2016 - 2022) scope. We identified the four largest monophyletic sequence clusters in the core genome phylogeny that are represented by prominent sequence types (ST): BAPS1 (mainly ST95), BAPS4 (mainly ST73), BAPS10 (mainly ST131), BAPS14 (mainly ST58). We show that the four dominant clusters vary in different characteristics of recombination: number of single nucleotide polymorphisms due to recombination, number of recombination blocks, cumulative bases in recombination blocks, ratio of probabilities that a given site was altered through recombination and mutation (r/m), and ratio of rates at which recombination and mutation occurred (ρ/θ). Each sequence cluster contains a unique set of antimicrobial resistance (AMR) and virulence genes that have experienced recombination. Common among the four sequence clusters were the recombined virulence genes with functions associated with the Curli secretion channel (csgG) and ferric enterobactin transport (entEF, fepEG). We did not identify any one recombined AMR gene that was present in all four sequence clusters. However, AMR genes mdtABC, baeSR, emrKY and tolC had experienced recombination in sequence clusters BAPS4, BAPS10, and BAPS14. These differences lie in part on the contributions of vertically inherited ancestral recombination and contemporary branch-specific recombination, with some genomes having relatively higher proportions of recombined DNA.

conclusionsOur results highlight the variation in the propensity to exchange DNA via homologous recombination within a distinct population at narrow geographic and temporal ranges. Understanding the sources of the genetic variation in invasive E. coli will help inform the implementation of effective strategies to reduce the burden of disease and AMR.

Indexed as

Escherichia coliHomologous RecombinationRecombination, GeneticEscherichia coli InfectionsGenetic VariationGenome, BacterialHumansPhylogenyPolymorphism, Single NucleotideAntimicrobial resistanceBloodstream infectionEscherichia coliGenomeHomologous recombinationSequence types

Identifiers

PMID39994515
PMCPMC11853335

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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.