ArticleNucleic acids research2012
Detection of recombination events in bacterial genomes from large population samples.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers, 1 of them a synthesis that pooled it.
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Who cites it
132 citing papers in PubMed, 1 synthesis or guideline pooled it, 202 citations in OpenAlex.
- One hypervirulent clone, sequence type 283, accounts for a large proportion of invasive Streptococcus agalactiae isolated from humans and diseased tilapia in Southeast Asia.PLoS neglected tropical diseases · 2019Pooled it
- Multidrug resistant Pseudomonas aeruginosa in Estonian hospitals.BMC infectious diseases · 2018Trial
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- Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215.BMC microbiology · 2024Article
- Evolution of homologous recombination rates across bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Core genes can have higher recombination rates than accessory genes within global microbial populations.eLife · 2022Article
- Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022Review
- Horizontal gene transfer and adaptive evolution in bacteria.Nature reviews. Microbiology · 2022Review
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- Emergence and Expansion of a Carbapenem-Resistant Pseudomonas aeruginosa Clone Are Associated with Plasmid-BornemSystems · 2021Article
- Genome-wide insights into population structure and host specificity of Campylobacter jejuni.Scientific reports · 2021Article
- Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data.Journal of microbiology (Seoul, Korea) · 2021Review
- Molecular Characterization ofFrontiers in microbiology · 2021Article
- Characteristics of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae and Contact to Animals in Estonia.Microorganisms · 2020Article
- A coarse-graining, ultrametric approach to resolve the phylogeny of prokaryotic strains with frequent homologous recombination.BMC evolutionary biology · 2020Article
- Plasmids Shaped the Recent Emergence of the Major Nosocomial Pathogen Enterococcus faecium.mBio · 2020Article
- Reconstruction of Dispersal Patterns of Hypervirulent Meningococcal Strains of Serogroup C:cc11 by Phylogenomic Time Trees.Journal of clinical microbiology · 2019Article
- Chicken Meat-Associated Enterococci: Influence of Agricultural Antibiotic Use and Connection to the Clinic.Applied and environmental microbiology · 2019Article
- Population Gene Introgression and High Genome Plasticity for the Zoonotic Pathogen Streptococcus agalactiae.Molecular biology and evolution · 2019Article
72 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
Abstract
Analysis of important human pathogen populations is currently under transition toward whole-genome sequencing of growing numbers of samples collected on a global scale. Since recombination in bacteria is often an important factor shaping their evolution by enabling resistance elements and virulence traits to rapidly transfer from one evolutionary lineage to another, it is highly beneficial to have access to tools that can detect recombination events. Multiple advanced statistical methods exist for such purposes; however, they are typically limited either to only a few samples or to data from relatively short regions of a total genome. By harnessing the power of recent advances in Bayesian modeling techniques, we introduce here a method for detecting homologous recombination events from whole-genome sequence data for bacterial population samples on a large scale. Our statistical approach can efficiently handle hundreds of whole genome sequenced population samples and identify separate origins of the recombinant sequence, offering an enhanced insight into the diversification of bacterial clones at the level of the whole genome. A data set of 241 whole genome sequences from an important pandemic lineage of Streptococcus pneumoniae is used together with multiple simulated data sets to demonstrate the potential of our approach.
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Registered trials
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.