Genomic Epidemiology of Bacterial Infections
Summary
Genomic epidemiology of bacterial infections harnesses the power of whole-genome sequencing to resolve patterns of pathogen transmission, evolution and antimicrobial resistance with unprecedented precision. By comparing genomic data from clinical and environmental isolates, researchers can reconstruct transmission chains, distinguish outbreak strains from background noise and monitor the emergence and spread of resistant clones across regions and host species. This discipline bridges laboratory microbiology, bioinformatics and public health, offering a high-resolution alternative to traditional phenotypic typing methods. In recent years, falling costs and increased throughput of sequencing technologies have enabled routine application in hospital outbreak investigations, national surveillance frameworks and global networks. Genomic data inform infection prevention strategies by pinpointing sources of nosocomial transmission, guiding antimicrobial stewardship and updating intervention policies in near real time. On a broader scale, integration of bacterial genomics with epidemiological metadata underpins One Health approaches, illuminating the flow of resistance determinants between humans, animals and the environment. As databases of bacterial genomes grow, phylogenetic analyses yield insights into the evolutionary forces—such as recombination, mutation and horizontal gene transfer—that drive pathogen adaptation. Together, these advances transform our understanding of bacterial disease dynamics, strengthen surveillance systems and support evidence-based public health interventions worldwide.
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Genomic Epidemiology of Bacterial Infections publication trend
The graph below shows the total number of articles in genomic epidemiology of bacterial infections across all publications each year (not limited to Nature Index journals).
Technical terms
Whole-genome sequencing: Determination of the complete DNA sequence of a bacterial genome, enabling comprehensive analysis of genetic variation.
De novo assembly: Reconstruction of a genome sequence from sequencing reads without using a reference genome, often necessary for poorly characterised species.
Antimicrobial resistance (AMR): The ability of bacteria to survive or grow in the presence of drugs designed to inhibit or kill them, often driven by specific genetic mutations or mobile resistance elements.
Phylogenetic analysis: Comparison of genetic sequences to infer evolutionary relationships among bacterial isolates, used to reconstruct transmission histories.
Genomic surveillance: Systematic collection and analysis of pathogen genomic data to monitor emergence, spread and evolution of infectious agents in populations.
References
- Genomics for public health and international surveillance of antimicrobial resistance. The Lancet Microbe (2023).
- Hound: a novel tool for automated mapping of genotype to phenotype in bacterial genomes assembled de novo. Briefings in Bioinformatics (2024).
- Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens. Microbiology (2018).
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