ReviewClinical microbiology reviews2016
A Primer on Infectious Disease Bacterial Genomics.
Review in Clinical microbiology reviews, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
18 citing papers in PubMed.
- Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach.BMC genomics · 2023Article
- Article
- Genomic Investigation of Carbapenem-ResistantGenes · 2021Article
- Molecular Characterization of Multidrug-ResistantFrontiers in microbiology · 2021Article
- Article
- Molecular Epidemiology of Carbapenemases inAntibiotics (Basel, Switzerland) · 2020Review
- Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory.Clinical microbiology reviews · 2020Review
- Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework.BMC bioinformatics · 2019Article
- Article
- Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria.Microbial genomics · 2019Article
- Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective.BMC genomics · 2018Article
- chewBBACA: A complete suite for gene-by-gene schema creation and strain identification.Microbial genomics · 2018Article
- MentaLiST - A fast MLST caller for large MLST schemes.Microbial genomics · 2018Article
- New Insights intoFrontiers in microbiology · 2018Article
- SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology.Microbial genomics · 2017Article
- Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access.Frontiers in microbiology · 2017Review
- Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.Frontiers in microbiology · 2017Article
- Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology.Frontiers in microbiology · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time. Here, we present a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provide a general understanding of the analytical concepts to develop a workflow that will meet the objectives and goals of HTS projects.
Indexed as
Identifiers
What OpenQuestion holds
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.