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pip:fct16713_2024 [2026/05/29 18:00] ramirez [Summary] |
pip:fct16713_2024 [2026/06/08 09:38] (current) ramirez [RESONANCE - Promoting large-scale use of genomics in understanding bacterial pathogen dynamics and evolution] |
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| FCT reference: 2023.16713.ICDT/LISBOA2030-FEDER-00866000 | FCT reference: 2023.16713.ICDT/LISBOA2030-FEDER-00866000 | ||
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| + | [[https://doi.org/10.54499/2023.17805.ICDT|doi:10.54499/2023.17805.ICDT]] | ||
| Principal investigator: M. Ramirez | Principal investigator: M. Ramirez | ||
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| Identification and tracking of bacterial pathogens are essential for outbreak investigations, epidemiological surveillance, and understanding pathogen evolution. The current proposal will create software facilitating the genomic surveillance of novel pathogens, expanding the discrimination of existing systems and facilitating leveraging the population information to design novel prophylactic and diagnostic approaches. | Identification and tracking of bacterial pathogens are essential for outbreak investigations, epidemiological surveillance, and understanding pathogen evolution. The current proposal will create software facilitating the genomic surveillance of novel pathogens, expanding the discrimination of existing systems and facilitating leveraging the population information to design novel prophylactic and diagnostic approaches. | ||
| - | ===== Summary ===== | + | ===== Outline ===== |
| The identification and tracking of microbial strains or lineages have become indispensable for a multitude of applications, including outbreak investigations, epidemiological surveillance, and understanding microbial evolution. This information has been translated into more informed public health decisions, including measures for outbreak prevention and control or the development and application of new diagnostic and therapeutic approaches. Genomics quickly became the paradigm for these activities and assumed a pivotal role in public health preparedness, prevention, and response. High throughput sequencing (HTS), generating high-quality draft or complete microbial genomes, decentralized and revolutionized these activities. The SARS-CoV-2 pandemic universalized access to HTS and raised the awareness of the benefits that could be reaped from genomic pathogen data. The continuous recognition of novel bacterial pathogens and the emergence of novel bacterial strains of public health concern alert to the fact that although “pathogen X” is usually taken to refer to viral threats, we should also prepare to address potential bacterial pathogens X, as recognized recently by the [[https://cdn.who.int/media/docs/default-source/blue-print/agenda_pathogen-x-august-2022_v8.pdf|WHO]]. | The identification and tracking of microbial strains or lineages have become indispensable for a multitude of applications, including outbreak investigations, epidemiological surveillance, and understanding microbial evolution. This information has been translated into more informed public health decisions, including measures for outbreak prevention and control or the development and application of new diagnostic and therapeutic approaches. Genomics quickly became the paradigm for these activities and assumed a pivotal role in public health preparedness, prevention, and response. High throughput sequencing (HTS), generating high-quality draft or complete microbial genomes, decentralized and revolutionized these activities. The SARS-CoV-2 pandemic universalized access to HTS and raised the awareness of the benefits that could be reaped from genomic pathogen data. The continuous recognition of novel bacterial pathogens and the emergence of novel bacterial strains of public health concern alert to the fact that although “pathogen X” is usually taken to refer to viral threats, we should also prepare to address potential bacterial pathogens X, as recognized recently by the [[https://cdn.who.int/media/docs/default-source/blue-print/agenda_pathogen-x-august-2022_v8.pdf|WHO]]. | ||
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| ==== Papers ==== | ==== Papers ==== | ||
| + | Mamede R, Vila-Cerqueira P, Carriço JA, [[people:ramirez|Ramirez M]]. 2026. <fc #0000FF>chewBBACA 3: lowering the barrier for scalable and detailed whole- and core-genome multilocus sequence typing</fc>. Genome Med 18:51. [[https://www.ncbi.nlm.nih.gov/pubmed/41877275/|(PMID: 41877275)]]. | ||
| ==== Meeting presentations ==== | ==== Meeting presentations ==== | ||