Research Topic

Bacterial Pathogen Genomics: Recent Achievements, Current Applications and Future Challenges

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Advances in whole genome sequencing (WGS) technologies have transformed the intersecting fields of clinical microbiology, molecular epidemiology and bacterial population genomics. The ultra-fine scale resolution provided by WGS data provides unprecedented power to detect and manage outbreaks in real-time, ...

Advances in whole genome sequencing (WGS) technologies have transformed the intersecting fields of clinical microbiology, molecular epidemiology and bacterial population genomics. The ultra-fine scale resolution provided by WGS data provides unprecedented power to detect and manage outbreaks in real-time, infer transmission pathways and identify likely sources. Epidemiological surveillance on both global and local scales focus on both the transmission of bacteria, as well as the genes and mobile genetic elements (MGEs) they carry that confer antimicrobial resistance or heightened virulence. High throughput and routine genome sequencing linked to reference laboratories has informed and streamlined therapeutic approaches and infection control strategies, and the implementation of WGS in agricultural and environmental settings has helped to broaden disease management to encapsulate the “One Health” concept. However, challenges remain in the optimization, standardization and repeatability of community-oriented bioinformatics platforms and tools required to fully exploit this new technology for the purposes of:

- Understanding the transmission dynamics of both pathogens and mobile genetic elements (MGEs) they carry
- Detection of pathogens and/or resistance genes by sentinel epidemiological surveillance in health-care, community, agricultural and environmental settings
- Reliable genotype-to-phenotype predictions and genome-wide association studies (GWAS)
- Bacterial population structure, gene-flow, pan-genome dynamics and adaptation.

There is now a growing number of WGS-based applications (both experimental and bioinformatic) supporting bacterial pathogen characterization and typing, and these are critical for genome-based pathogen surveillance. However, methodological standards are quickly changing with advances in technological achievements, and the rapidly changing bioinformatic landscape raises major challenges in the international standardization and harmonization.

This research topic welcomes original research, review, mini-review, Hypothesis and Theory, Perspective, and Opinion articles that focus on the applications, challenges and limitations of all aspects of WGS-based pathogen characterization and genome-based surveillance (“genomic epidemiology”). This Research Topic includes, but is not limited to:

- Analysis of bacterial outbreaks (tools and applications)
- Transmission analysis (strains and MGEs)
- Genotype-phenotype predictions
- GWAS applications in bacteria
- Novel genomic structure analysis based on WGS
- “One Health” perspectives on disease management based on WGS
- Aspects sequencing-based applications including (clinical) metagenomics for diagnostics and typing
- Databases and modeling

Frontiers in Microbiology does not publish genome announcements, and this collection does not include descriptive studies that report sequencing data unless they are accompanied by clear hypothesis and experiments and provide insight into the microbiological system or process under study.


Keywords: Pathogen Genomics, Whole Genomic Sequencing, One Health Concept


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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