ReviewEuropean journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology2017
Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review.
Review in European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 2 of them syntheses that pooled it.
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
60 citing papers in PubMed, 2 syntheses or guidelines pooled it, 128 citations in OpenAlex.
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- The Role of Genital Tract Microbiome in Fertility: A Systematic Review.International journal of molecular sciences · 2021Pooled it
- Mapping the resistance landscape: A large-scale study of polymyxin-resistant pathogens circulating in low-and middle-income countries.Research square · 2026Article
- Phenotypic, Genetic, and Virulence Characterization ofPathogens (Basel, Switzerland) · 2026Article
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- Ribotyping for Accurate Identification of Infectious Bacteria in Animal-Derived Foods and Laboratory Samples: Implications for Human Health.Journal of tropical medicine · 2026Review
- Interpreting antimicrobial resistance from bacterial whole-genome sequencing: prediction tools, database fragmentation, analytical trade-offs, and harmonized reporting.Frontiers in microbiology · 2026Review
- Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.Antibiotics (Basel, Switzerland) · 2025Review
- Genomic Epidemiology of ESBL- and Carbapenemase-Producing Enterobacterales in a Spanish Hospital: Exploring the Clinical-Environmental Interface.Microorganisms · 2025Article
- Metagenomic Next-Generation Sequencing in Infectious Diseases: Clinical Applications, Translational Challenges, and Future Directions.Diagnostics (Basel, Switzerland) · 2025Review
- Genomic diversity and tracing ofMicrobial genomics · 2025Article
- Unlocking the Interactions Between the Whole-Body Microbiome and HPV Infection: A Literature Review.Pathogens (Basel, Switzerland) · 2025Review
- Global spread of Streptococcus pyogenes A genomics-supported narrative review.FEMS microbiology reviews · 2025Review
- Antimicrobial resistance at a turning point: microbial drivers, one health, and global futures.Frontiers in microbiology · 2025Review
- Next generation sequencing as a panacea for antibiotic susceptibility testing: yea or nay?Frontiers in public health · 2025Article
- Multilocus sequence typing and phenotypic properties of Streptococcus mutans from Thai children with different caries statuses.BMC oral health · 2024Article
- Potential Convergence to Accommodate Pathogenicity Determinants and Antibiotic Resistance Revealed inMicroorganisms · 2024Article
- Pathogenicity and Genomic Characteristics Analysis ofMicroorganisms · 2024Article
- The zoonotic pathogen Wohlfahrtiimonas chitiniclastica - current findings from a clinical and genomic perspective.BMC microbiology · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.
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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.