ArticleMicrobial genomics2021
Bacterial genomic epidemiology with mixed samples.
Article in Microbial genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 44 citations in OpenAlex.
- Genetic strategies for sex-biased persistence of gut microbes across human life.Nature communications · 2023Pooled it
- A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producingMicrobial genomics · 2026Article
- Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli.Nature microbiology · 2026Article
- Sequence type and strain-level detection ofMicrobial genomics · 2026Article
- Environmental surveillance of bacteria in a new intensive care unit using plate sweeps.Microbial genomics · 2026Article
- Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult.Nature communications · 2025Article
- Genomic diversity of non-typhoidalMicrobial genomics · 2025Article
- Population sequencing for phylogenetic diversity and transmission analyses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.Nature microbiology · 2025Article
- Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements.Nature microbiology · 2025Article
- Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm.Genome research · 2025Article
- Efficient and robust search of microbial genomes via phylogenetic compression.Nature methods · 2025Article
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- Bacterial strain sharing between humans, animals, and the environment among urban households.medRxiv : the preprint server for health sciences · 2024Article
- Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan.Nature communications · 2024Article
- What are the missing pieces needed to stop antibiotic resistance?Microbial biotechnology · 2023Review
- Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT.Genome research · 2023Article
- Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes.Bioinformatics (Oxford, England) · 2023Article
- Strong pathogen competition in neonatal gut colonisation.Nature communications · 2022Article
- Distribution and Current State of Molecular Genetic Characterization in Pathogenic Free-Living Amoebae.Pathogens (Basel, Switzerland) · 2022Review
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 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstrate the effectiveness of our approach using closely related samples in a nosocomial setting, obtaining results that are comparable to those based on single-colony picks. Our results lend firm support to more widespread consideration of genomic epidemiology with mixed infection samples.
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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.