ArticleGenome research2015
Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers, 2 of them syntheses that pooled it.
What it found
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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.
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.
Who cites it
98 citing papers in PubMed, 2 syntheses or guidelines pooled it, 164 citations in OpenAlex.
- Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages.Clinical microbiology reviews · 2019Pooled it
- Epidemic potential of Escherichia coli ST131 and Klebsiella pneumoniae ST258: a systematic review and meta-analysis.BMJ open · 2016Pooled it
- Infection mechanisms ofiMeta · 2026Article
- Genetic traits of IncK2 plasmids and theMicrobial genomics · 2026Article
- Bacterial genome-wide association studies: exploring the genetic variation underlying bacterial phenotypes.Applied and environmental microbiology · 2025Review
- Abundance of fecal indicator bacteria and diversity of Escherichia coli associated with poultry farms and pasture land cover in streams of northwestern South Carolina.Environmental monitoring and assessment · 2024Article
- A gentle introduction to pangenomics.Briefings in bioinformatics · 2024Review
- Article
- Population structure and antibiotic resistance of swine extraintestinal pathogenic Escherichia coli from China.Nature communications · 2024Article
- Distribution ofInternational journal of molecular sciences · 2024Article
- Clinical and Genomic Characterization of a Cohort of Patients With Klebsiella pneumoniae Bloodstream Infection.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2024Article
- Longitudinal molecular analysis of clinical and fecalFrontiers in microbiology · 2024Article
- Genome-Wide Association Studies (GWAS) Approaches for the Detection of Genetic Variants Associated with Antibiotic Resistance: A Systematic Review.Microorganisms · 2023Review
- The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans.PLoS genetics · 2023Article
- Article
- Blood Culture Negative Endocarditis: A Review of Laboratory Diagnostic Approaches.International journal of general medicine · 2023Review
- Whole genome sequence analysis of ESBL-producingMicrobial genomics · 2022Article
- Low levels of tetracyclines select for a mutation that prevents the evolution of high-level resistance to tigecycline.PLoS biology · 2022Article
- The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France.Applied and environmental microbiology · 2022Article
- Use of Large-Scale Genomics to Identify the Role of Animals and Foods as Potential Sources of Extraintestinal Pathogenic Escherichia coli That Cause Human IllnessFoods (Basel, Switzerland) · 2022Article
38 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
Large-scale bacterial genome sequencing efforts to date have provided limited information on the most prevalent category of disease: sporadically acquired infections caused by common pathogenic bacteria. Here, we performed whole-genome sequencing and de novo assembly of 312 blood- or urine-derived isolates of extraintestinal pathogenic (ExPEC) Escherichia coli, a common agent of sepsis and community-acquired urinary tract infections, obtained during the course of routine clinical care at a single institution. We find that ExPEC E. coli are highly genomically heterogeneous, consistent with pan-genome analyses encompassing the larger species. Investigation of differential virulence factor content and antibiotic resistance phenotypes reveals markedly different profiles among lineages and among strains infecting different body sites. We use high-resolution molecular epidemiology to explore the dynamics of infections at the level of individual patients, including identification of possible person-to-person transmission. Notably, a limited number of discrete lineages caused the majority of bloodstream infections, including one subclone (ST131-H30) responsible for 28% of bacteremic E. coli infections over a 3-yr period. We additionally use a microbial genome-wide-association study (GWAS) approach to identify individual genes responsible for antibiotic resistance, successfully recovering known genes but notably not identifying any novel factors. We anticipate that in the near future, whole-genome sequencing of microorganisms associated with clinical disease will become routine. Our study reveals what kind of information can be obtained from sequencing clinical isolates on a large scale, even well-characterized organisms such as E. coli, and provides insight into how this information might be utilized in a healthcare setting.
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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.