ReviewPathogens (Basel, Switzerland)2014
WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare?
Review in Pathogens (Basel, Switzerland), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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.
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.
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Who cites it
28 citing papers in PubMed.
- Targeted next-generation sequencing for antimicrobial resistance detection in ventilator-associated pneumonia.Frontiers in cellular and infection microbiology · 2025Article
- Detecting antibiotic resistance: classical, molecular, advanced bioengineering, and AI-enhanced approaches.Frontiers in microbiology · 2025Review
- Recent development and fighting strategies for lincosamide antibiotic resistance.Clinical microbiology reviews · 2024Review
- CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter.BMC bioinformatics · 2023Article
- Whole-genome sequence analysis through online web interfaces: a review.Genomics & informatics · 2022Article
- Article
- A classification framework forEvolutionary applications · 2020Article
- The use of next generation sequencing for improving food safety: Translation into practice.Food microbiology · 2019Review
- Development of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella.PloS one · 2019Article
- A Metataxonomic Tool to Investigate the Diversity ofFrontiers in microbiology · 2019Article
- Assessment and Comparison of Molecular Subtyping and Characterization Methods forFrontiers in microbiology · 2019Review
- GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015.Microbial genomics · 2018Article
- Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes.Journal of clinical microbiology · 2018Article
- Article
- Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory.Journal of clinical microbiology · 2017Article
- Genomic sequencing of Neisseria gonorrhoeae to respond to the urgent threat of antimicrobial-resistant gonorrhea.Pathogens and disease · 2017Review
- Mycobacterium tuberculosis resistance prediction and lineage classification from genome sequencing: comparison of automated analysis tools.Scientific reports · 2017Article
- Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer.Scientific reports · 2017Article
- Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii.PloS one · 2017Article
- A Primer on Infectious Disease Bacterial Genomics.Clinical microbiology reviews · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in DNA sequencing technologies have the potential to transform the field of clinical and public health microbiology, and in the last few years numerous case studies have demonstrated successful applications in this context. Among other considerations, a lack of user-friendly data analysis and interpretation tools has been frequently cited as a major barrier to routine use of these techniques. Here we consider the requirements of microbiology laboratories for the analysis, clinical interpretation and management of bacterial whole-genome sequence (WGS) data. Then we discuss relevant, existing WGS analysis tools. We highlight many essential and useful features that are represented among existing tools, but find that no single tool fulfils all of the necessary requirements. We conclude that to fully realise the potential of WGS analyses for clinical and public health microbiology laboratories of all scales, we will need to develop tools specifically with the needs of these laboratories in mind.
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.