ArticleGenome medicine2014
Clinical detection and characterization of bacterial pathogens in the genomics era.
Article in Genome medicine, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT03532438 (Whole Genome Sequencing of Nontuberculous Mycobacterium), which is not on this map. Cited by 54 papers, 3 of them syntheses that pooled it.
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.
Whole Genome Sequencing of Nontuberculous Mycobacterium (NTM) Derived From Sputum Specimen of NTM Lung Disease Patients Living Together and From Their Environmental Samples
Who cites it
54 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Genetic Fingerprint ofPathogens (Basel, Switzerland) · 2026Pooled it
- Recent advances in surface enhanced Raman spectroscopy for bacterial pathogen identifications.Journal of advanced research · 2023Pooled it
- Bacterial infections in acute exacerbation of chronic obstructive pulmonary disease: a systematic review and meta-analysis.Infection · 2020Pooled it
- First comprehensive whole genome sequencing report of a multidrug-resistantNew microbes and new infections · 2026Article
- Omics and Multiomics-Based Diagnostics for Invasive Candidiasis: Toward Precision Medicine.Molecular & cellular proteomics : MCP · 2025Review
- Utilizing large and diverse bacterial genome datasets to improve the detection and identification ofMicrobial genomics · 2025Article
- Antimicrobial Resistance, Virulence Gene Profiling, and Spa Typing ofPathogens (Basel, Switzerland) · 2025Article
- Review
- Microbes and pathogens associated with shrimps - implications and review of possible control strategies.Frontiers in Marine Science · 2024Article
- Addressing the Knowledge Deficit in Hospital Bed Planning and Defining an Optimum Region for the Number of Different Types of Hospital Beds in an Effective Health Care System.International journal of environmental research and public health · 2023Review
- Article
- Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis.BMC infectious diseases · 2023Observational
- Application of next-generation sequencing to identify different pathogens.Frontiers in microbiology · 2023Review
- Clinical metagenomics-challenges and future prospects.Frontiers in microbiology · 2023Review
- Next-Generation Sequencing Applications for the Study of Fungal Pathogens.Microorganisms · 2022Review
- Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method.mSphere · 2022Article
- What Can Genetics Do for the Control of Infectious Diseases in Aquaculture?Animals : an open access journal from MDPI · 2022Review
- Neurosyphilis with a rare magnetic resonance imaging pattern confirmed by metagenomic next-generation sequencing: a case report.European journal of medical research · 2022Article
- Prevalence and Molecular Characterization ofAnimals : an open access journal from MDPI · 2022Article
- High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance.Computational and structural biotechnology journal · 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
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The availability of genome sequences obtained using next-generation sequencing (NGS) has revolutionized the field of infectious diseases. Indeed, more than 38,000 bacterial and 5,000 viral genomes have been sequenced to date, including representatives of all significant human pathogens. These tremendous amounts of data have not only enabled advances in fundamental biology, helping to understand the pathogenesis of microorganisms and their genomic evolution, but have also had implications for clinical microbiology. Here, we first review the current achievements of genomics in the development of improved diagnostic tools, including those that are now available in the clinic, such as the design of PCR assays for the detection of microbial pathogens, virulence factors or antibiotic-resistance determinants, or the design of optimized culture media for 'unculturable' pathogens. We then review the applications of genomics to the investigation of outbreaks, either through the design of genotyping assays or the direct sequencing of the causative strains. Finally, we discuss how genomics might change clinical microbiology in the future.
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.