ArticleCell host & microbe2020
A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation.
Article in Cell host & microbe, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 129 papers.
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Who cites it
129 citing papers in PubMed, 220 citations in OpenAlex.
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- Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils.Nature microbiology · 2026Article
- Genomic Epidemiology of FoodborneAntibiotics (Basel, Switzerland) · 2026Article
- Identification of the Integration/Excision Module and Regulatory Elements Involved in the Mobility of IME8, an Integrative and Mobilizable Element From Mosquitocidal Lysinibacillus sphaericus.Microbial biotechnology · 2026Article
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- Establishment of the chromid database and analysis of evolutionary research.Molecular genetics and genomics : MGG · 2026Article
- Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation.Nature microbiology · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Whole genome investigation of multi-drug resistant Staphylococcus aureus strain.World journal of microbiology & biotechnology · 2026Article
- Metagenomic analysis of antimicrobial resistance, virulence, and mobile genetic elements in the gut microbiota of Caprinae species.Communications biology · 2026Article
- Comprehensive genomic characterization and public health implications of multidrug-resistant Escherichia coli from poultry in Noakhali, Bangladesh.BMC microbiology · 2026Article
- The plasmid-host fitness landscape: a new paradigm for predicting the fate of mobile resistance.Applied and environmental microbiology · 2026Review
- Type VI secretion system completeness shapes evolutionary trade-offs in theFrontiers in microbiology · 2026Article
- Isolation and whole-genome characterization of multidrug-resistant Acinetobacter baumannii from Indian retail meat: unveiling high-risk clones and zoonotic transmission threats via comparative genomics.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Cross-sectional comparative shotgun metagenomic analysis of the subgingival resistome in healthy subjects and patients with periodontitis from four countries.Journal of oral microbiology · 2026Article
- Coexistence of carbapenemase and hypervirulence-associated genes amongFrontiers in microbiology · 2026Article
- Deciphering the Genomic Traits of Multi-Enterocin-ProducingMicroorganisms · 2025Article
69 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Mobile genetic elements (MGEs) contribute to bacterial adaptation and evolution; however, high-throughput, unbiased MGE detection remains challenging. We describe MGEfinder, a bioinformatic toolbox that identifies integrative MGEs and their insertion sites by using short-read sequencing data. MGEfinder identifies the genomic site of each MGE insertion and infers the identity of the inserted sequence. We apply MGEfinder to 12,374 sequenced isolates of 9 prevalent bacterial pathogens, including Mycobacterium tuberculosis, Staphylococcus aureus, and Escherichia coli, and identify thousands of MGEs, including candidate insertion sequences, conjugative transposons, and prophage elements. The MGE repertoire and insertion rates vary across species, and integration sites often cluster near genes related to antibiotic resistance, virulence, and pathogenicity. MGE insertions likely contribute to antibiotic resistance in laboratory experiments and clinical isolates. Additionally, we identified thousands of mobility genes, a subset of which have unknown function opening avenues for exploration. Future application of MGEfinder to commensal bacteria will further illuminate bacterial adaptation and evolution.
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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.