ArticleThe Journal of antimicrobial chemotherapy2014
Rapid single-colony whole-genome sequencing of bacterial pathogens.
Article in The Journal of antimicrobial chemotherapy, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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.
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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
35 citing papers in PubMed, 56 citations in OpenAlex.
- AEmerging microbes & infections · 2026Article
- Genomic structure ofMicrobial genomics · 2026Article
- Prevalence of diphtheria and antimicrobial-resistant wound infections among asylum seekers in Heidelberg, Germany, August-October 2024.PloS one · 2026Article
- Article
- High density genomic surveillance and risk profiling of clinical Listeria monocytogenes subtypes in Germany.Genome medicine · 2024Article
- Recent Advances in Nanotechnology for the Management ofBiosensors · 2022Review
- Petri-plate, bacteria, and laser optical scattering sensor.Frontiers in cellular and infection microbiology · 2022Review
- A common protocol for the simultaneous processing of multiple clinically relevant bacterial species for whole genome sequencing.Scientific reports · 2021Article
- Identification of Shiga Toxin-Producing Escherichia coli Outbreaks Using Whole Genome Sequencing.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Quantifying the transmission of antimicrobial resistance at the human and livestock interface with genomics.Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases · 2020Review
- A nosocomial cluster of vancomycin resistant enterococci among COVID-19 patients in an intensive care unit.Antimicrobial resistance and infection control · 2020Article
- Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory.Clinical microbiology reviews · 2020Review
- Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields.BMC bioinformatics · 2020Article
- Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes.Scientific reports · 2019Article
- Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.Genome biology · 2019Article
- Role of NS5A-L31/Y93 Double Wild-type in Failure of Glecaprevir/Pibrentasvir Double Therapy in Two Patients with a History of Direct-acting Antiviral Agent Failure: An Ultra-deep Sequencing Analysis.Internal medicine (Tokyo, Japan) · 2019Article
- Rapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory.The Journal of antimicrobial chemotherapy · 2019Article
- Article
- Article
- Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens.Microbiology (Reading, England) · 2018Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 1 country.
Funding
Abstract
objectivesAs a result of the introduction of rapid benchtop sequencers, the time required to subculture a bacterial pathogen to extract sufficient DNA for library preparation can now exceed the time to sequence said DNA. We have eliminated this rate-limiting step by developing a protocol to generate DNA libraries for whole-genome sequencing directly from single bacterial colonies grown on primary culture plates.
methodsWe developed our protocol using single colonies of 17 bacterial pathogens responsible for severe human infection that were grown using standard diagnostic media and incubation conditions. We then applied this method to four clinical scenarios that currently require time-consuming reference laboratory tests: full identification and genotyping of salmonellae; identification of blaNDM-1, a highly transmissible carbapenemase resistance gene, in Klebsiella pneumoniae; detection of genes encoding staphylococcal toxins associated with specific disease syndromes; and monitoring of vaccine targets to detect vaccine escape in Neisseria meningitidis.
resultsWe validated our single-colony whole-genome sequencing protocol for all 40 combinations of pathogen and selective, non-selective or indicator media tested in this study. Moreover, we demonstrated the clinical value of this method compared with current reference laboratory tests.
conclusionsThis advance will facilitate the implementation of whole-genome sequencing into diagnostic and public health microbiology.
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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.