Pathogen Genomics: Empowering Infectious Disease Surveillance and Outbreak Investigations

With progress in high throughput nucleic acid sequencing technology, comparative microbial genomics is increasingly used for high resolution epidemiological investigation of sources and transmission dynamics of infectious agents and antimicrobial resistance determinants in humans, animals, and environmental reservoirs. Whole genome sequencing in combination with epidemiological investigations has shown unprecedented precision and accuracy in delineating transmission pathways, and revealing sources of endemic and epidemic infections and emergence of novel and drug resistant pathogens. Efforts are ongoing, however, to streamline and fine-tune the laboratory workflows, bioinformatics tools, and data governance required for real time outbreak studies and surveillance at local, national, and international levels. Solutions to key semantic and logistic bottlenecks are in development and under trial across the world in partnership between academia, industry, and government. These include design of user-friendly, biologically robust genomic /genetic allele type nomenclature for human and zoonotic pathogens, access to accurate phenotype (resistome, virulome, antigenic variants) prediction algorithms and adaptive knowledge bases as well computational infrastructure enabling multi-centre WGS data sharing for surveillance and alert with adequate personal data protection. The increasing uptake of culture-independent testing by pathology providers has been recognized internationally as the existential threat to public health laboratory surveillance. Novel metagenomics-based approaches of direct culture-independent sequencing can assist in future-proofing of public health surveillance.

This Research Topic will assess the new knowledge gained by innovative genomic epidemiological methods on sources and mechanisms of transmission of human and zoonotic pathogens and antimicrobial resistance of clinical and public health importance. It will also examine recent experience in translating advances in genomics and metagenomics into communicable disease control and the emerging organizational models for and impact of public health applications of these novel approaches to inform disease prevention and control.

This article collection will cover studies on genomic micro-evolution, phylodynamics, and epidemiology of human pathogens (bacteria, viruses, and parasites), including state of the art applications based on culture-based and culture-independent genome sequencing to infection source attribution, outbreak investigations, infection control, and public health genomic surveillance. Systematic reviews, narrative reviews, and perspective manuscripts are welcome.