ReviewClinical microbiology reviews2017
Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis.
Review in Clinical microbiology reviews, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 247 papers, 2 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
247 citing papers in PubMed, 2 syntheses or guidelines pooled it, 443 citations in OpenAlex.
- Systematic review: genotypic and phenotypic resistance of fluoroquinolone-resistantFrontiers in veterinary science · 2025Pooled it
- Human microbiome and microbiota identification for preventing and controlling healthcare-associated infections: A systematic review.Frontiers in public health · 2022Pooled it
- A Simplified Guide to Whole-Genome Sequence Analysis of Salmonella on the Command Line.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Convergent methodologies in prosthetic joint infection research: integrating transdisciplinary approaches to understand and prevent biofilm-driven failure of orthopaedic prostheses.Journal of medical microbiology · 2026Review
- Forensic Microbiomics and Trace Microbial Evidence: Molecular Innovations for Linking Suspects, Objects, and Environments.Microorganisms · 2026Review
- Antibiotic profiles and draft genome sequences of fourMicrobiology resource announcements · 2026Article
- Genomic regulation of the diphtheria toxin gene and Its implications for molecular diagnostics and surveillance in low-resource settings.Molecular biology reports · 2026Review
- Review
- Responsible Use of Large Language Models in Microbial Genomics and Bioinformatics: A Life-Science Framework for Reliability, Reproducibility, and Risk-Aware Interpretation.Life (Basel, Switzerland) · 2026Review
- Comparative Genomic Analysis of Pseudomonas shahriarae Reveals Virulence Potential, Antimicrobial Resistance, and Environmental Adaptation.Current microbiology · 2026Article
- Strategies for integrating whole-genome sequencing into antimicrobial resistance surveillance.BMC genomics · 2026Review
- Article
- Genomic characterization of clinical isolates of carbapenem-resistantJAC-antimicrobial resistance · 2026Article
- Detecting healthcare-associated transmission and antifungal resistance inJournal of clinical microbiology · 2026Article
- Emerging zoonotic risks: whole-genome sequencing reveals antimicrobial resistance and genomic diversity in Providencia stuartii isolated from broiler chickens in Noakhali, Bangladesh.Poultry science · 2026Article
- Revealing genetic variation of Actinobacillus pleuropneumoniae Korean isolates using whole genome sequence analysis.Journal of microbiology (Seoul, Korea) · 2026Article
- Decoding the genome of Bacillus thuringiensis subsp. israelensis VCRC B668 to understand its mosquitocidal potential for biopesticide development.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Prediction of genetic relatedness ofAntimicrobial agents and chemotherapy · 2026Article
- Fast hospital discharge rates blur within-hospital 'transmission footprint' in bacterial genomes, as showcased with Staphylococcus aureus.PLoS computational biology · 2026Article
- Comparative genomics insights into Pseudomonas rhodesiae: environmental distribution, resistance determinants, virulence factors, and evolutionary implications.BMC genomics · 2026Article
187 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.
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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.