ArticleNature communications2022
Strong pathogen competition in neonatal gut colonisation.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 2 of them syntheses that pooled it.
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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.
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Who cites it
29 citing papers in PubMed, 2 syntheses or guidelines pooled it, 54 citations in OpenAlex.
- Neonatal Colonization With Antibiotic-Resistant Pathogens in Low- and Middle-Income Countries: A Systematic Review and Meta-Analysis.JAMA network open · 2024Pooled it
- Genetic strategies for sex-biased persistence of gut microbes across human life.Nature communications · 2023Pooled it
- Microbial-derived tryptophan metabolites in the infant gut associate with increased risk of asthma following cesarean section.Nature communications · 2026Article
- Mapping the evolutionary path towards multi-drug resistance in the pandemicMicrobial genomics · 2026Article
- Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli.Nature microbiology · 2026Article
- Tracing the early bacterial settlers in preterm and very-low birth-weight infants: first report of microbiota dynamics in South American neonates.Infection and immunity · 2026Article
- Sequence type and strain-level detection ofMicrobial genomics · 2026Article
- Machine learning-based lineage prediction from antimicrobial susceptibility testing phenotypes forMicrobial genomics · 2026Article
- Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces.Probiotics and antimicrobial proteins · 2026Article
- Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones.Nature communications · 2025Article
- Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation.NPJ biofilms and microbiomes · 2025Article
- Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.Nature microbiology · 2025Article
- Analysis of ESAC-Net/EARS-Net Data from 29 EEA Countries for Spatiotemporal Associations Between Antimicrobial Use and Resistance-Implications for Antimicrobial Stewardship?Antibiotics (Basel, Switzerland) · 2025Article
- Plasmid-driven strategies for clone success in Escherichia coli.Nature communications · 2025Article
- Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA).Molecular biology and evolution · 2025Article
- Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series.The ISME journal · 2025Article
- Residence-colonization trade-off and niche differentiation enable coexistence of Escherichia coli phylogroups in healthy humans.The ISME journal · 2025Article
- Mobile genetic elements: the hidden puppet masters underlying infant gut microbiome assembly?Microbiome research reports · 2025Article
- Lactobacillus rhamnosus modulates murine neonatal gut microbiota and inflammation caused by pathogenic Escherichia coli.BMC microbiology · 2024Article
- Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly.Nature microbiology · 2024Article
Corrections and comments
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Authors and funding
12 authors at 6 institutions in 3 countries.
Funding
Abstract
Opportunistic bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and the relationship of colonisation potential to prevalence in disease, and how ecological factors might be modulating these. Here, using a combination of latest high-resolution metagenomics and strain-level genomic epidemiology methods we performed a characterisation of the competition and colonisation dynamics for a longitudinal cohort of neonatal gut microbiomes. We found strong inter- and intra-species competition dynamics in the gut colonisation process, but also a number of synergistic relationships among several species belonging to genus Klebsiella, which includes the prominent human pathogen Klebsiella pneumoniae. No evidence of preferential colonisation by hospital-adapted pathogen lineages in either vaginal or caesarean section birth groups was detected. Our analysis further enabled unbiased assessment of strain-level colonisation potential of extra-intestinal pathogenic Escherichia coli (ExPEC) in comparison with their propensity to cause bloodstream infections. Our study highlights the importance of systematic surveillance of bacterial gut pathogens, not only from disease but also from carriage state, to better inform therapies and preventive medicine in the future.
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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.